Class II human histone deacetylases, and uses related thereto

ABSTRACT

The invention provides histone deacetylase class II nucleic acids and polypeptides, methods and reagents for their use, and related compounds including small molecule libraries containing class II histone deacetylase inhibitors.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional of and claims priority under 35 U.S.C.§120 to U.S. patent application Ser. No. 13/324,036, filed Dec. 13,2011, now U.S. Pat. No. 8,435,780, which is a divisional of and claimspriority under 35 U.S.C. §120 to U.S. patent application Ser. No.12/370,390, filed Feb. 12, 2009, now U.S. Pat. No. 8,076,116, which is acontinuation of and claims priority under 35 U.S.C. §120 to U.S. patentapplication Ser. No. 11/831,303, filed Jul. 31, 2007, now abandoned,which is a continuation of and claims priority under 35 U.S.C. §120 toU.S. patent application Ser. No. 10/964,313, filed Oct. 13, 2004, nowU.S. Pat. No. 7,250,504, which is a continuation of and claims priorityunder 35 U.S.C. §120 to U.S. patent application Ser. No. 09/800,187,filed Mar. 5, 2001, now abandoned, which claims priority under 35 U.S.C.§119(e) to U.S. Provisional patent application, U.S. Ser. No.60/186,802, filed Mar. 3, 2000, each of which is incorporated herein byreference.

GOVERNMENT FUNDING

This invention was made with government support under grant numberGM38617 awarded by the National Institute of General Medical Sciences.The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

The regulation and mechanism of transcription has been of great interestto researchers. In eukaryotic cells, DNA is packaged in the form ofnucleosomal arrays. Each nucleosome core consists of 145 base pairs ofDNA wound around an octarner of H2A, H2B, H3 and H4 histone proteins.These nucleosome cores are then packaged into higher order structureswith additional factors to form chromatin (Luger, K. et al. Nature,1997, 389, 251-60).

The incorporation of DNA into chromatin creates a repressive environmentthat has been implicated in transcriptional silencing. Two cellularprocesses serve to alter chromatin structure (Workman et al., Annu. Rev.Biochem, 1998, 67, 545-579). Chromatin remodeling factors such asSWI/SNF, RSC, NURF, and NRD (reviewed in Varga-Weisz, P. D. and Becker,P. B. Curr. Opin. Cell Biol., 1998, 10, 346-353; see also, Tong et al.Nature, 1998, 395, 917-921; Zhang et al. Cell, 1998, 95, 279-289; Xue etal., Mol. Cell, 1998, 2, 851-861) have been shown to increase theaccessibility of the DNA, presumably by modifications of the nucleosomalstructure. A second cellular mechanism involves alterations of theacetylation state of nucleosomal histones. Hypoacetylated chromatin isoften associated with silent genes, while hyperacetylation is correlatedwith actively transcribed genes. However, this rule is not absolute.Acetylation of K12 on histone H4 is observed in silent heterochromatinregions in Drosophila and yeast (reviewed in Grunstein, M. Nature, 1997,389, 349-352). Furthermore, there is increasing evidence for regulationof non-histone proteins by acetylation, and this may function inactivation as well as repression of transcription (see, Imhof et al.,Curr. Biol., 1997, 7, 689-692; Gu, W. and Roeder, R. G. Cell, 1997, 90,595-606; Munshi et al. Mol. Cell, 1998, 2, 457-467). The acetylationstate of histones and perhaps non-histone proteins is regulated by adynamic interaction of histone acetyltransferase (HAT) and histonedeacetylase (HDAC) enzymes.

Previously, three human HDACs (Taunton, J. et al. Science, 1996, 272,408-411; Yang et al. J. Biol. Chem., 1997, 272, 28001-28007; Emiliani etal. Proc. Natl. Acad. Sci. USA, 1998, 95, 2795-2800; Dagond et al.Biochem. Biophys. Res. Commun., 1998, 242, 648-652) and five yeast HDACs(see, Rundlett et al. Proc. Natl. Acad. Sci USA, 1996, 93, 14503-14508;Carmen et al. J. Biol. Chem., 1996, 271, 15837-15844) had beenidentified and several of these were biochemically characterized. TheseHDACs, together with the prokaryotic enzymes acetylspermine deacetylase(ASD) and acetoin utilization protein (acuC) comprise a deacetylasesuperfamily. In yeast, members of this superfamily can be subdividedinto two classes based on size and sequence considerations, as well asthe observation that Rpd3p and Hda1p function in biochemically distinctcomplexes. The first class (I) consists of Rpd3p, Hos1p, and Hos2p,while the second class contains Hda1p. Similarly in mammals, HDAC1,HDAC2 and HDAC3 conform to class I criteria, while no human class IIHDAC proteins have been identified previously.

Clearly, the identification of alternate classes of genes encodinghistone deacetylase proteins would aid in the investigation of functionsfor these protein products, and thus would be of great benefit in thecontrol of gene transcription and the cell cycle.

SUMMARY OF THE INVENTION

In recognition of the desire to understand the cellular function andregulation of histone deacetylases, the present invention, in oneaspect, provides heretofore unidentified histone deacetylase genes, andgene products, expressed in mammals. In general, the invention providesa novel class of isolated HDx polypeptides, preferably recombinantand/or substantially pure preparations of one or more of the subject HDxpolypeptides. The invention also provides recombinantly produced HDxpolypeptides. In other embodiments, the HDx polypeptides of the presentinvention bind to 14-3-3 proteins, such binding resulting in regulationof cellular localization of the HDx protein. Additionally, in certainother embodiments, the HDx polypeptides of the present inventionassociated with other HDx polypeptides of this novel class and regulateHDAC function by protein pairing

In preferred embodiments, the invention features human class II HDACnucleic acids and polypeptides. For example, the nucleic acid of SEQ IDNO. 1 encodes HDAC4 and is substantially identical to GenBank AccessionNo. XM_(—)002252; and the polypeptide of SEQ ID NO. 2 corresponds toHDAC4 and is substantially identical to GenBank Accession No.XP_(—)002252. The nucleic acid of SEQ ID NO. 3 encodes HDAC5 and issubstantially identical to GenBank Accession No. XM_(—)008359; and thepolypeptide of SEQ ID NO. 4 corresponds to HDAC5 and is substantiallyidentical to GenBank Accession No. XP_(—)008359.2. The nucleic acid ofSEQ ID NO. 5 encodes HDAC6 and is substantially identical to GenBankAccession No. NM_(—)006044; and the polypeptide of SEQ ID NO. 6 encodesHDAC6 and is substantially identical to NP_(—)006035.2.

In still other embodiments, the invention features HDAC7-type humanclass II HDAC nucleic acids and polypeptides, including both HDAC7A andHDAC7B. HDAC7A is encoded by the nucleic acid of SEQ ID NO. 11 and whichis substantially identical to GenBank Accession No. XM_(—)007047. Theamino acid sequence of HDAC7A is represented in SEQ ID NO. 12 and issubstantially identical to GenBank Accession No. XP_(—)007047.1. HDAC7Bis encoded by the nucleic acid of SEQ ID NO. 13 and which issubstantially identical to GenBank Accession No. XM_(—)004963. The aminoacid sequence of HDAC7A is represented in SEQ ID NO. 14 and issubstantially identical to GenBank Accession No. XP_(—)004963.2.

The HDx polypeptides disclosed herein are capable of modulatingproliferation, survival and/or differentiation of cells, inter aliabecause of their ability to alter chromatin structure by deacetylatinghistones. In preferred embodiments the polypeptide has a biologicalactivity including an ability to deacetylate an acetylated histonesubstrate, preferably a substrate analog of histone H3 and/or H4. Inother embodiments the HDx polypeptides of the present invention bind totrapoxin or to trichostatin, such binding resulting in the inhibition adeacetylase activity of the HDx polypeptide. However, HDx polypeptideswhich specifically antagonize such activities, such as may be providedby dominant negative mutants, are also specifically contemplated.

In addition to acting as a deacetylating enzymes, the HDx polypeptidesof the present invention are also involved in a novel mechanism forcontrolling the activity of HDAC proteins. In certain embodiments,polypeptides of the present invention are able to interact with 14-3-3proteins, whereby cellular localization is regulated. Moreover, inpreferred embodiments, the subject HDx proteins have the ability tomodulate cell growth by influencing cell cycle progression or tomodulate gene transcription.

In one embodiment, the polypeptide is identical with or homologous to anHDx protein. Exemplary HDx polypeptides include amino acid sequencesrepresented in any one of SEQ ID Nos. 2, 4 or 6. Related members of theHDx family are also contemplated, for instance, an HDx polypeptidepreferably has an amino acid sequence at least 80% homologous to apolypeptide represented by one of more of the polypeptides designated inSEQ ID: Nos: 2, 4, or 6, though polypeptides with higher sequencehomologies of, for example, 85%, 90%, 95% or 98% are also contemplated.In one embodiment, the HDx polypeptide is encoded by a nucleic acidwhich hybridizes under stringent conditions with a nucleic acid sequencerepresented in one or more of SEQ ID Nos: 1, 3 or 5. Homologs of thesubject HDx proteins also include versions of the protein which areresistant to post-translation modification, as for example, due tomutations which alter modification sites (such as tyrosine, threonine,serine or asparagine residues), or which inactivate an enzymaticactivity associated with the protein.

The HDx polypeptide can comprise a full length protein, such asrepresented in SEQ ID Nos. 2, 4 or 6, or it can comprise a fragmentcorresponding to particular motifs/domains (for example, a ν motif suchas shown in SEQ ID Nos, 7, 8, 9 or 10), or to arbitrary sizes, e.g., atleast 5, 10, 25, 50, 100, 150 or 200 amino acids in length. In preferredembodiments, the polypeptide, or fragment thereof, specificallydeacetylates histones. In other preferred embodiments, the HDxpolypeptide includes at least one ν motif and in certain embodimentsincludes two ν motifs.

In certain preferred embodiments, the invention features a purified orrecombinant HDx polypeptide having a molecular weight in the range of 80kDa to 150 kDa. It will be understood that certain post-translationalmodifications, e.g., phosphorylation, prenylation and the like, canincrease the apparent molecular weight of the HDx protein relative tothe unmodified polypeptide chain.

The subject proteins can also be provided as chimeric molecules, such asin the form of fusion proteins. For instance, the HDx protein can beprovided as a recombinant fusion protein which includes a secondpolypeptide portion, e.g., a second polypeptide having an amino acidsequence unrelated (heterologous) to the HDx polypeptide, e.g., thesecond polypeptide portion is glutathione-S-transferase, e.g., thesecond polypeptide portion is an epitope tage.

In yet another embodiment, the invention features a nucleic acidencoding an HDx polypeptide, or polypeptide homologous thereto, whichpolypeptide has the ability to modulate, e.g., either mimic orantagonize, at least a portion of the activity of a wild-type HDxpolypeptide. Exemplary HDx-encoding nucleic acid sequences arerepresented by SEQ ID Nos: 1, 3 or 5.

In another embodiment, the nucleic acid of the present inventionincludes a coding sequence which hybridizes under stringent conditionswith one or more of the nucleic acid sequences in SEQ ID. Nos. 1, 3 or5. The coding sequence of the nucleic acid can comprise a sequence whichis identical to a coding sequence represented in one of SEQ ID Nos. 1, 3or 5, or it can merely be homologous to one or more of these sequences.In preferred embodiments, the nucleic acid encodes a polypeptide whichspecifically modulates, by acting as either an agonist or antagonist,the enzymatic activity of an HDx polypeptide.

Furthermore, in certain preferred embodiments, the subject HDx nucleicacid will include a transcriptional regulatory sequence, e.g., at leastone of a transcriptional promoter or transcriptional enhancer sequence,which regulatory sequence is operably linked to the HDx gene sequence.Such regulatory sequences can be used to render the HDx gene sequencesuitable for use as an expression vector. This invention alsocontemplates the cells transfected with said expression vector whetherprokaryotic or eukaryotic and a method for producing HDx proteins byemploying said expression vectors.

In yet another embodiment, the nucleic acid hybridizes under stringentconditions to a nucleic acid probe corresponding to at least 12consecutive nucleotides of either sense or antisense sequence of one ormore of SEQ ID Nos.: 1, 3 or 5; and more preferably to at least 20. 30,40 or 50 consecutive (e.g., contiguous) nucleotides; and more preferablyto at least 100, 200 or 300 consecutive nucleotides of either sense orantisense sequence of one or more of SEQ ID Nos. 1, 3, or 5.

Yet another aspect of the present invention concerns an immunogencomprising an HDx polypeptide in an immunogenic preparation, theimmunogen being capable of eliciting an immune response specific for anHDx polypeptide; e.g. a humoral response, e.g. an antibody response;e.g. a cellular response. In preferred embodiments, the immunogencomprising an antigenic determinant, e.g. a unique determinant, from aprotein represented by one of SEQ ID Nos. 2, 4, 6, 7, 8, 9 or 10.

A still further aspect of the present invention features antibodies andantibody preparations specifically reactive with an epitope of the HDximmunogen.

The invention also features transgenic non-human animals, e.g., mice,rats, rabbits, chickens, frogs or pigs, having a transgene, e.g.,animals which include (and preferably express) a heterologous form of anHDx gene described herein, or which misexpresses an endogenous HDx gene,e.g., an animal in which expression of one or more of the subject HDxproteins is disrupted. Such a transgenic animal can serve as an animalmodel for studying cellular and tissue disorders comprising mutated ormis-expressed HDx alleles or for use in drug screening.

The invention also provides a probe/primer comprising a substantiallypurified oligonucleotide, wherein the oligonucleotide comprises a regionof nucleotide sequence which hybridizes under stringent conditions to atleast 12 consecutive nucleotides of sense or antisense sequence of SEQID Nos: 1, 3 or 5, and more preferably to at least 30, 40, 50, 100, 200or 300 contiguous nucleotides of said sequences.

Nucleic acid probes which are specific for each of the HDx proteins arecontemplated by the present invention, e.g., probes which can discernbetween nucleic acid encoding a human or bovine HD. In preferredembodiments, the probe/primer further includes a label group attachedthereto and able to be detected. The label group can be selected, e.g.,from a group consisting of radioisotopes, fluorescent compounds,enzymes, and enzyme co-factors. Probes of the invention can be used as apart of a diagnostic test kit for identifying dysfunctions associatedwith mis-expression of an HDx protein, such as for detecting in a sampleof cells isolated from a patient, a level of a nucleic acid encoding asubject HDx protein; e.g., measuring an HDx mRNA level in a cell, ordetermining whether a genomic HDx gene has been mutated or deleted.These so called “probes/primers” of the invention can also be used as apart of “antisense” therapy which refers to administration or in situgeneration of oligonucleotide probes or their derivatives whichspecifically hybridize (e.g., bind) under cellular conditions, with thecellular mRNA and/or genomic DNA encoding one or more of the subject HDxproteins so as to inhibit expression of that protein, e.g., byinhibiting transcription and/or translation. Preferably, theoligonucleotide is at least 12 nucleotides in length, though primers of25, 40, 50, or 75 nucleotides in length are also contemplated.

In yet another aspect, the invention provides an assay for screeningtest compounds for inhibitors, or alternatively, potentiators, or aninteraction between an HDx protein and an HDx binding protein or nucleicacid sequence. An exemplary method includes the steps of (I) combiningan HDx polypeptide or fragment thereof, an HDx target polypeptide (suchas a histone, a 14-3-3 protein, a MEF2 transcription factor, aretinoblastoma associated protein such as RbAp48, or fragment thereofwhich interacts with the HDx protein), and a test compound, e.g., underconditions wherein, but for the test compound, the HDx protein and thetarget polypeptide are able to interact; and (ii) detecting theformation of a complex which includes the HDx protein and the targetpolypeptide either by directly quantitating the complex, the deacetylaseactivity of the HDx protein, or by measuring inductive effects of theHDx protein. A statistically significant change, such as a decrease, inthe formation of a complex in the presence of a test compound (relativeto what is seen in the absence of a test compound) is indicative of amodulation, e.g., inhibition, of the interaction between the HDx proteinand its target polypeptide.

In a particularly preferred embodiment, the invention providescombinatorial chemical libraries of compounds for screening for specificinhibitors of class II Histone Deacetylases (HDACs). The combinatoriallibraries are used in the assays of the invention in order to identifyHDAC inhibitors, including inhibitors specific to all class II histonedeacetylases and inhibitors specific to individual class II histonedeacetylases. The combinatorial libraries of the invention comprise aplurality of compounds represented by the structures #1, #2, and #3shown in FIG. 14A and the structure shown in FIG. 14B. In preferredembodiments, the plurality of compounds are spatially segregated.

Furthermore, the present invention contemplates the use of otherhomologs of the HDx polypeptides or bioactive fragments thereof togenerate similar assay formats. In one embodiment, the drug screeningassay can be derived with a fungal homolog of an HDx protein, such asRPD3, in order to identify agents which selectively inhibit the fungalhistone acetylase and not the human enzyme, e.g., for use as antifungalagents.

Yet another aspect of the present invention concerns a method formodulating one or more of growth, differentiation, or survival of amammalian cell by modulating HDx bioactivity, e.g., by inhibiting thedeacetylase activity of HDx proteins, or disrupting certainprotein-protein interactions. In general, whether carried out in vivo,in vitro, or in situ, the method comprises treating the cell with aneffective amount of an HDx therapeutic so as to alter, relative to thecell in the absence of treatment, at least one of (i) rate of growth;(ii) differentiation, or (iii) survival of the cell. Accordingly, themethod can be carried out with HDx therapeutics such as peptide andpeptidomimetics or other molecules identified in the above-referencedrug screens which antagonize the effects of naturally occurring HDxprotein on said cell. Other HDx therapeutics include antisenseconstructs for inhibiting expression of HDx proteins, and dominantnegative mutants of HDx proteins which competitively inhibitprotein-substrate and/or protein-protein interactions upstream anddownstream of the wild-type HDx protein.

In an exemplary embodiment the subject method is used to treat tumorcells by antagonizing HDx activity and blocking cell cycle progression.In one embodiment, the subject method includes the treatment oftesticular cells, so as to modulate spermatogenesis. In anotherembodiment, the subject method is used to modulate osteogenesis,comprising the treatment of osteogenic cells with an HDx polypeptide.Likewise, where the treated cell is a chondrogenic cell, the presentmethod is used to modulate chondrogenesis. In still another embodiment,HDx polypeptides can be used to modulate the differentiation ofprogenitor cells, e.g., the method can be used to cause differentiationof a hematopoietic cells, neuronal cells, or other stem/progenitor cellpopulations, to maintain a cell in a differentiated state, and/or toenhance the survival of a differentiated cell, e.g., to preventapoptosis, or other forms of cell death.

In addition to such HDx therapeutic uses, anti-fungal agents developedwith such screening assays as described herein can be used, for example,as preservatives in foodstuff, feed supplement for promoting weight gainin livestock, or in disinfectant formulations for treatment ofnon-living matter, e.g., for decontaminating hospital equipment androoms. In similar fashion, assays provided herein will permit selectionof deacetylase inhibitors which discriminate between the human andinsect deacetylase enzymes. Accordingly, the present invention expresslycontemplates the use and formulations of the deacetylase inhibitors ininsecticides, such as for use in management of insects like the fruitfly. Moreover, certain of the inhibitors can be selected on the basis ofinhibitory specificity for plant HDx-related activities relative to themammalian enzymes. Thus, the present invention specifically contemplatesformulations of deacetylase inhibitors for agricultural applications,such as in the form of a defoliant or the like.

The present method is applicable, for example, to cell culturetechnique, such as in the culturing of hematopoietic cells and othercells whose survival or differentiative state is dependent on HDxfunction. Moreover, HDx agonists and antagonists can be used fortherapeutic intervention, such as to enhance survival and maintenance ofcells, as well as to influence organogenic pathways, such as tissuepatterning and other differentiation processes. In an exemplaryembodiment, the method is practiced for modulating, in an animal, cellgrowth, cell differentiation or cell survival, and comprisesadministering a therapeutically effective amount of an HDx polypeptideto alter, relative to the absence of HDx treatment, at least one of (I)rate of growth; (ii) differentiation; or (iii) survival of one or morecell-types in the animal.

Another aspect of the present invention provides a method of determiningif a subject, e.g., a human patient, is at risk for a disordercharacterized by unwanted cell proliferation or aberrant control ofdifferentiation. The method includes detecting, in a tissue of thesubject, the presence or absence of a genetic lesion characterized by atleast one of (I) a mutation of a gene encoding an HDx protein, e.g.,represented in one of SEQ ID Nos. 2, 4, 6, 7, 8, 9, or 10 or a homologthereof; or (ii) the mis-expression of an HDx gene. In preferredembodiments, detecting the genetic lesion includes ascertaining theexistence of at least one of; a deletion of one or more nucleotides froman HDx gene; an addition of one or more nucleotides to the gene, asubstitution of one or more nucleotides of the gene, a gross chromosomalrearrangement of the gene; an alteration in the level of a messenger RNAtranscript of the gene; the presence of a non-wild type splicing patternof a messenger RNA transcript of the gene; or a non-wild type level ofthe protein.

For example, detecting the genetic lesion can include (I) providing aprobe/primer including an oligonucleotide containing a region ofnucleotide sequence which hybridizes to a sense or antisense sequence ofan HDx gene, e.g., a nucleic acid represented in one of SEQ ID Nos. 1, 3or 5 or naturally occurring mutants thereof, or 5 or 3′ flankingsequences naturally associated with the HDx gene; (ii) exposing theprobe/primer to nucleic acid of the tissue; and (iii) detecting, byhybridization of the probe/primer to the nucleic acid, the presence orabsence of the genetic lesion; e.g. wherein detecting the lesioncomprises utilizing the probe/primer to determine the nucleotidesequence of the HDx gene and, optionally, of the flanking nucleic acidsequences. For instance, the probe/primer can be employed in apolymerase chain reaction (PCR) or in a ligation chain reaction (LGR).In alternate embodiments, the level of an HDx protein is detected in animmunoassay using an antibody which is specifically immunoreactive withthe HDx protein.

DESCRIPTION OF THE DRAWING

FIGS. 1A-1D Predicted amino acid sequences of human class II histonedeacetylases. The conserved residues of the catalytic domains arehighlighted. (A) HDAC4 (SEQ ID NO:2) (B) HDAC5 (SEQ ID NO:4) (C) HDAC6(SEQ ID NO:6) predicted amino acid sequences. Note that there are twoputative catalytic domains in HDAC6. (D) Alignment of catalytic domainsof yeast HDA1p (SEQ ID NO:16), human HDAC1 (SEQ ID NO:15), 4 (SEQ IDNO:8), and 5 (SEQ ID NO:9) with both catalytic regions of HDAC6 (SEQ IDNO:10 and residues 610-683 of SEQ ID NO:6, respectively). The residuesthat are conserved in these HDACs as well as in acuC (B. subtilis,Accession 348052) and ASD (M. ramosa, Accession 3023317) are in boldtype, and those residues that are conserved within the Class II humanHDAC enzymes are boxed.

FIGS. 2A and 2B. Expression analysis of novel human Class II HDAC familymembers. Multiple human tissue northern blots were probed to determinemRNA expression of HDAC4, HDAC5, and HDAC6. Blots were stripped andreprobed with (β-actin cDNA to normalize for total mRNA. The position ofmolecular size markers is indicated to the left.

FIGS. 3A and 3B. Class II HDAC enzymes deacetylate all four corehistones in vitro. Recombinant FLAG-tagged HDACs were immunoprecipitatedfrom transfected Jurkat cell extracts using α-FLAG antibody (Sigma).Immunopurified enzymes were incubated with radiolabeled core histones asdescribed in Methods. (A) The HDAC activity was measured byscintillation counting of the released [³H]-acetic acid. Whereindicated, immunoprecipitates were preincubated with trichostatin A(Wako) prior to addition of histones. Each assay was performed induplicate and averaged. (B) Substrate specificity of class II HDACs.Deacetylase reactions were separated by 20% SDS/PAGE and stained withCoomassie (top). The gel was treated with EnHance (NationalDiagnostics), dried and exposed to film (bottom). The identities of thecore histones are indicated to the left. RbAp48 was transfected as anegative control.

FIGS. 4A and 4B. The catalytic domains of HDACb function independently.The histidine residues homologous to H141 of HDAC1 in each of thecatalytic domains (H216 and H611) were mutated to alanine by PCR overlapextension. The single and double mutants were FLAG-tagged and expressedin Tag-Jurkat cells. The enzymes were immunoprecipitated using α-FLAGantibodies (Sigma) and expression levels were compared by Westernblotting (A). The mutant enzymes were then assayed for histonedeacetylase activity as before (B).

FIGS. 5A and 5B. Class II HDAC enzymes and HDAC1 are in differentcomplexes in vivo. Recombinant FLAG-tagged HDACs were precipitated fromtransfected Jurkat cell extracts using α-FLAG antibody (Sigma),separated by SDS/PAGE and subjected to Western blot analysis. Blots wereprobed with (A) α-FLAG antibody (Sigma) to determine expression levelsand (B) α-CHD4, α-mSin3A, α-MTA, α-HDAC1, αHDAC3 and α-Rbp48 antibodiesto determine if these proteins co-immunoprecipitated with the Class IIHDAC enzymes.

FIGS. 6A and 6B. Sequence analysis suggests that HDAC enzymes havediverged into two classes. (A) (SEQ ID NOS:17-25, respectively)Alignment of human HDAC enzymes 1 through 6 with yeast Rpd3p, Hos1p,Hos2p, Hos3p, M. ramosa ASD, and B. subtilis acuC reveals the presenceof seven conserved regions, whose consensus sequences differ between thetwo classes. Amino acids are represented by single letter codes; Xrepresents any amino acid while Φ indicates a hydrophobic residue.NF=not found. (B) A phylogenetic analysis suggests that the HDAC enzymesdiverged from a common prokaryotic ancestor to form two classes of HDACproteins. Proteins from three different phyla were examined. Prokaryoticproteins are preceded by (pro), yeast proteins are preceded by y, whilehuman proteins are capitalized. Note that yHos3p does not correlate wellwith either HDAC class.

FIGS. 7A and 7B. Association of 11DAC4 and HDAC5 with two isoforms of14-3-3.

A) Recombinant, FLAG-tagged HDAC1 and HDAC4 were transiently expressedin TAg Jurkat cells and immunoprecipitated using α-FLAG agarose (Sigma).Mock-transfected cells were used as a negative control. Theimmunopurified complexes were separated by SDS/PAGE and the proteinswere visualized by silver stain. Two novel bands at 30 and 32 kDa in theHDAC4 immunoprecipitate were identified as 14-3-3 β and ε by peptidemicrosequencing analysis,

B) The association between HDAC4 and HDAC5 with 14-3-3 was confirmed byWestern blot analysis. The recombinant FLAG-tagged proteins wereimmunoprecipitated with α-FLAG agarose and the purified complexes wereseparated by SDS/PAGE. The presence of HDAC3, 14-3-3 β and ε wasconfirmed by probing with specific antibodies (Santa Cruz).

FIGS. 8A and 8B. Nuclear-cytoplasmic shuttling of HDAC4 and HDAC5 iscorrelated to 14-3-3 expression levels

A) Recombinant HDAC4-EGFP and HDAC5-EGFP were transiently expressed inU2OS cells and the localization of the protein was observed byfluorescence microscopy.

B) Overexpression of 14-3-3 β causes an increased cytoplasmiclocalization of HDAC4-EGPF. U2OS cells were transiently transfected withHDAC4-EGFP and either a control plasmid (pcDNA3.1, Invitrogen) ormyc-tagged 14-3-3 β. Forty-eight hours post-transfection, the cells werefixed with paraformaldehyde and probed with an α-myc antibody (UpstateBiotechnology) and an α-mouse Ig Texas Red conjugated secondary antibody(Sigma). The DNA was stained with Hoechst dye (Molecular Probes).

FIGS. 9A and 9B. Phosphorylation-dependent binding of 14-3-3 to HDAC4and HDAC5

A) Association of HDAC4 and HDAC5 with 14-3-3 and HDAC3 is dependent onthe phosphorylation state of the proteins. HDAC4-FLAG and HDAC5-FLAGwere transiently expressed in TAg Jurkat cells. Forty-eight hourspost-transfection, the cells were treated for 1.5 hours withstaurosporine and calyculin A. The immunopurified HDAC4-FLAG andHDAC5-FLAG complexes were subjected to Western blot analysis and testedfor HDAC activity, as described in the experimental procedures. The HDACactivity was measured by scintillation counting of the released[³H]-acetic acid.

B) The binding of 14-3-3 to HDAC4 prevents interaction with importin α.Forty-eight hours after transfection with HDAC4-FLAG, TAg Jurkat cellswere treated with staurosporin or calyculin A for 1.5 hours. HDAC4-FLAGwas immunopurified and subjected to Western blot analysis withα-importin α antibodies (Transducin Laboratories).

FIG. 10. Schematic representation of HDLP-TSA complex interactions. TheTSA HDAC inhibitor is shown bound to HPLP (C7-C15 of TSA are labeled).The surrounding HDLP residues are labelled and the corresponding HDAC1active site residues are indicated below in parentheses. The Zn²⁺ cationin the active site of HDLP is shown as a filled circle. Thatchedsemi-circles indicate van der Waals contacts between hydrophobic proteinresides and TSA, while hydrogen bonds are shown as dashed lines.

FIGS. 11A-11C. Proposed catalytic mechanism for deacetylation ofacetylated lysine. HDLP active site residues and their proposed HDACcounterparts (in parentheses) are labelled.

FIG. 12. General structural feature of HDAC inhibitors. The generalstructural features of HDAC inhibitors include a Cap group which can bevaried to optimize inhibition of a particular HDAC or class of HDACs, analiphatic chain and a functional group which interacts with the activesite of the HDAC.

FIGS. 13A and 13B. Alterations in residues contacting TSA in humanHDACs. The residues contacting TSA in HDLP are those which are bothshaded and labelled with a consensus residue (i.e. P22 and Y91 residuesin the rim of channel, GI40, F141, F198, and L265 residues in thechannel, and 11131, 132, D166, D168, 11170, D258, and Y297 residues inthe active site) is shown. The surrounding resides that differ betweenclass I and class II HDACs are shaded and labelled with an asterisk (*).(SEQ ID NOS:26-73, respectively.)

FIGS. 14A and 14B. HDAC inhibitor small molecule libraries. Thegeneralized structures of two representative HDAC inhibitor compoundlibraries are shown.

FIG. 15. Representative positive from HDAC6 screen of printed library.Cy5HDAC was used to screen the printed 1,3-dioxane library. Arepresentative positive (compound 4-P9) from this screen is shown.

FIG. 16. Affect of representative compounds on HDAC1 and HDAC6 activity.

FIG. 17. Retesting of resynthesized 11-A15.

DEFINITIONS

For convenience, certain terms employed in the specification, examplesand appended claims are collected here.

As used herein, the “HDx” polypeptides and nucleic acids of theinvention include the histone deacetylace (“HDAC”) class II polypeptideand nucleic acid sequences disclosed herein and “HDx” and “HDAC” areused interchangeably.

As used herein, the term “nucleic acid” refers to polynucleotides suchas deoxyribonucleic acid (DNA), and, where appropriate, ribonucleic acid(RNA). The term should also be understood to include, as equivalents,analogs of either RNA or DNA made from nucleotide analogs, and, asapplicable to the embodiment being described, single (sense orantisense) and double-stranded polynucleotides.

As used herein, the term “gene” or “recombinant gene” refers to anucleic acid comprising an open reading frame encoding one of the novelclass of HDx polypeptides of the present invention, including both exonand (optionally) intron sequences. A “recombinant gene” refers tonucleic acid encoding an HDx polypeptide and comprising HDx-encodingexon sequences, though it may optionally include intron sequences whichare either derived from a chromosomal HDx gene or from an unrelatedchromosomal gene. Exemplary recombinant genes encoding the subject HDxpolypeptide are represented in the appended Sequence Listing. The term“intron” refers to a DNA sequence present in a given HDx gene which isnot translated into protein and is generally found between exons.

As used herein, the term “transfection” means the introduction of anucleic acid, e.g., an expression vector, into a recipient cell bynucleic acid-mediated gene transfer. “Transformation”, as used herein,refers to a process in which a cell's genotype is changed as a result ofthe cellular uptake of exogenous DNA or RNA, and, for example, thetransformed cell expresses a recombinant form of an HDx polypeptide or,where antisense expression occurs from the transferred gene, theexpression of a naturally-occurring form of the HDx protein isdisrupted.

As used herein, the term “specifically hybridizes” refers to the abilityof the probe/primer of the invention to hybridize to at least 15consecutive nucleotides of an HDx gene, such as an HDx sequencedesignated in one of SEQ ID Nos: 1, 3 or 5, or a sequence complementarythereto, or naturally occurring mutants thereof, such that it has lessthan 15%, preferably less than 10%, and more preferably less than 5%background hybridization to a cellular nucleic acid (e.g., mRNA orgenomic DNA) encoding a protein other than an HDx protein, as definedherein. In preferred embodiments, the oligonucleotide probe specificallydetects only one of the subject HDx paralogs, e.g., does notsubstantially hybridize to transcripts for other HDx homologs in thesame species. In general, the term “specifically hybridizes” or“specifically detects” further refers to the ability of a nucleic acidmolecule of the invention to hybridize to at least approximately 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 100,150, 200, 300, 350, or 400 consecutive nucleotides of a vertebrate,preferably a HDAC gene. In certain instances the invention providesnucleic acids which hybridize under stringent conditions to a nucleicacid represented by SEQ ID Nos. 1, 3 or 5 or complement thereof or thenucleic acids. Appropriate stringency conditions which promote DNAhybridization, for example, 6.0× sodium chloride/sodium citrate (SSC) atabout 45° C., followed by a wash of 2.0×SSC at 50° C., are known tothose skilled in the art or can be found in Current Protocols inMolecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6 or inMolecular Cloning: A Laboratory Manual, Cold Spring Harbor Press (1989).For example, the salt concentration in the wash step can be selectedfrom a low stringency of about 2.0×SSC at 50° C. to a high stringency ofabout 0.2×SSC at 50° C. In addition, the temperature in the wash stepcan be increased from low stringency conditions at room temperature,about 22° C., to high stringency conditions at about 65° C. Bothtemperature and salt may be varied, or temperature and saltconcentration may be held constant while the other variable is changed.In a preferred embodiment, an htrb nucleic acid of the present inventionwill bind to one of SEQ ID Nos. 1, 3, or 5 or complement thereof undermoderately stringent conditions, for example at about 2.0×SSC and about40° C. In a particularly preferred embodiment, an HDAC nucleic acid ofthe present invention will bind to one of SEQ ID Nos. 1, 2, 3, or 4 orcomplement thereof under high stringency conditions. In anotherparticularly preferred embodiment, a HDAC nucleic acid sequence of thepresent invention will bind to one of SEQ ID Nos. 1, 3 or 5 whichcorrespond to the HDAC cDNA, preferably ORF nucleic acid sequences,under high stringency conditions.

As used herein, the term “vector” refers to a nucleic acid moleculecapable of transporting another nucleic acid to which it has beenlinked. One type of preferred vector is an episome, i.e., a nucleic acidcapable of extra-chromosomal replication. Preferred vectors are thosecapable of autonomous replication and/or expression of nucleic acids towhich they are linked. Vectors capable of directing the expression ofgenes to which they are operatively linked are referred to herein as“expression vectors”. In general, expression vectors of utility inrecombinant DNA techniques are often in the form of “plasmids” whichrefer generally to circular double stranded DNA loops which, in theirvector form are not bound to the chromosome. In the presentspecification, “plasmid” and “vector” are used interchangeably as theplasmid is the most commonly used form of vector. However, the inventionis intended to include such other forms of expression vectors whichserve equivalent functions and which become known in the artsubsequently hereto.

“Transcriptional regulatory sequence” is a generic term used throughoutthe specification to refer to DNA sequences, such as initiation signals,enhancers, and promoters, which induce or control transcription ofprotein coding sequences with which they are operable linked. Inpreferred embodiments, transcription of one of the recombinant HDx genesis under the control of a promoter sequence (or other transcriptionalregulatory sequence) which controls the expression of the recombinantgene in a cell-type which expression is intended. It will also beunderstood that the recombinant gene can be under the control oftranscriptional regulatory sequences which are the same or which aredifferent from those sequences which control transcription of thenaturally-occurring forms of HDx genes.

As used herein, the term “tissue-specific promoter” means a DNA sequencethat serves as a promoter, i.e., regulates expression of a selected DNAsequence operably linked to the promoter, and which effects expressionof the selected DNA sequence in specific cells of a tissue, such ascells of hepatic, pancreatic, neuronal or hematopoietic origin. The termalso covers so-called “leaky” promoters, which regulate expression of aselected DNA primarily in one tissue, but can cause at least low levelexpression in other tissues as well.

As used herein “transgenic animal” is any animal, preferably a non-humanmammal, bird or an amphibian, in which one or more of the cells of theanimal contain heterologous nucleic acid introduced by way of humanintervention, such as by transgenic techniques well known in the art.The nucleic acid is introduced into the cell, directly or indirectly byintroduction into a precursor of the cell, by way of deliberate geneticmanipulation, such as by microinjection or by infection with arecombinant virus. The term genetic manipulation does not includeclassical cross-breeding, or in vitro fertilization, but rather isdirected to the introduction of recombinant DNA molecule. This moleculemay be integrated within a chromosome, or it may be extrachromosomallyreplicating DNA. In the typical transgenic animals described herein, thetransgene causes cells to express a recombinant form of one of the HDxproteins, e.g., either agonistic or antagonistic forms. However,transgenic animals in which the recombinant HDx gene is silent are alsocontemplated, as for example, the FLP or CRE recombinase dependentconstructs described below. Moreover, “transgenic animal” also includesthose recombinant animals in which gene disruption of one or more HDxgenes is caused by human intervention, including both recombination andantisense techniques.

The “non-human animals of the invention include, but are not limited to,vertebrates such as rodents, non-human primates, sheep, dog, cow,chickens, amphibians, reptiles, etc. Preferred non-human animals areselected from the rodent family including rat and mouse, most preferablymouse, though transgenic amphibians, such as members of the Xenopusgenus, and transgenic chickens can also provide important tools forunderstanding and identifying agents which can affect, for example,embryogenesis and tissue formation. The invention also contemplatestransgenic insects, including those of the genus Drosophila, such as D.melanogaster. The term “chimeric animal” is used herein to refer toanimals in which the recombinant gene is found, or in which therecombinant gene is expressed in some but not all cells of the animal.The term “tissue-specific chimeric animal” indicates that one of therecombinant HDx genes is present and/or expressed or disrupted in sometissues but not others.

As used herein, the term “transgene” means a nucleic acid sequence(encoding, e.g., one of the HDx polypeptides, or pending an antisensetranscript thereto), which is partly or entirely heterologous, i.e.,foreign, to the transgenic animal or cell into which it is introduced,or, is homologous to an endogenous gene of the transgenic animal or cellinto which it is introduced, but which is designed to be inserted, or isinserted, into the animal's genome in such a way as to alter the genomeof the cell into which it is inserted (e.g., it is inserted at alocation which differs from that of the natural gene or its insertionresults in a knockout). A transgene can include one or moretranscriptional regulatory sequences and any other nucleic acid, such asintrons, that may be necessary for optimal expression of a selectednucleic acid.

As is well known, genes for a particular polypeptide may exist in singleor multiple copies within the genome of an individual. Such duplicategenes may be identical or may have certain modifications, includingnucleotide substitutions, additions or deletions, which all still codefor polypeptides having substantially the same activity. The term “DNAsequence encoding an HDx polypeptide” may thus refer to one or moregenes within a particular individual. Moreover, certain differences innucleotide sequences may exist between individuals of the same species,which are called alleles. Such allelic differences may or may not resultin differences in amino acid sequence of the encoded polypeptide yetstill encode a protein with the same biological activity.

The term “nucleotide sequence complementary to the nucleotide sequenceset forth in SEQ ID No. x” refers to the nucleotide sequence of thecomplementary strand of a nucleic acid strand having SEQ ID No. x. Theterm “complementary strand” is used herein interchangeably with the term“complement”. The complement of a nucleic acid strand can be thecomplement of a coding strand or the complement of a non-coding strand.When referring to double stranded nucleic acids, the complement of anucleic acid having SEQ ID No. x refers to the complementary strand ofthe strand having SEQ ID No. x or to any nucleic acid having thenucleotide sequence of the complementary strand of SEQ ID No. x. Whenreferring to a single stranded nucleic acid having the nucleotidesequence SEQ ID No. x, the complement of this nucleic acid is a nucleicacid having a nucleotide sequence which is complementary to that of SEQID No. x. The nucleotide sequences and complementary sequences thereofare always given in the 5′ to 3′ direction.

The term “percent identical” refers to sequence identity between twoamino acid sequences or between two nucleotide sequences. Identity caneach be determined by comparing a position in each sequence which may bealigned for purposes of comparison. When an equivalent position in thecompared sequences is occupied by the same base or amino acid, then themolecules are identical at that position; when the equivalent siteoccupied by the same or a similar amino acid residue (e.g., similar insteric and/or electronic nature), then the molecules can be referred toas homologous (similar) at that position. Expression as a percentage ofhomology, similarity, or identity refers to a function of the number ofidentical or similar amino acids at positions shared by the comparedsequences. Expression as a percentage of homology, similarity, oridentity refers to a function of the number of identical or similaramino acids at positions shared by the compared sequences. Variousalignment algorithms and/or programs may be used, including FASTA,BLAST, or ENTREZ. FASTA and BLAST are available as a part of the GCGsequence analysis package (University of Wisconsin, Madison, Wis.), andcan be used with, e.g., default settings. ENTREZ is available throughthe National Center for Biotechnology Information, National Library ofMedicine, National Institutes of Health, Bethesda, Md. In oneembodiment, the percent identity of two sequences can be determined bythe GCG program with a gap weight of 1, e.g., each amino acid gap isweighted as if it were a single amino acid or nucleotide mismatchbetween the two sequences.

Other techniques for alignment are described in Methods in Enzymology,vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996),ed. Doolittle, Academic Press, Inc., a division of Harcourt Brace & Co.,San Diego, Calif., USA. Preferably, an alignment program that permitsgaps in the sequence is utilized to align the sequences. TheSmith-Waterman is one type of algorithm that permits gaps in sequencealignments. See Meth. Mol. Biol. 70: 173-187 (1997). Also, the GAPprogram using the Needleman and Wunsch alignment method can be utilizedto align sequences. An alternative search strategy uses MPSRCH software,which runs on a MASPAR computer. MPSRCH uses a Smith-Waterman algorithmto score sequences on a massively parallel computer. This approachimproves ability to pick up distantly related matches, and is especiallytolerant of small gaps and nucleotide sequence errors. Nucleicacid-encoded amino acid sequences can be used to search both protein andDNA databases.

Databases with individual sequences are described in Methods inEnzymology, ed. Doolittle, supra. Databases include Genbank, EMBL, andDNA Database of Japan (DDBJ).

Preferred nucleic acids have a sequence at least 70%, and morepreferably 80% identical and more preferably 90% and even morepreferably at least 95% identical to an nucleic acid sequence of asequence shown in one of SEQ ID Nos. of the invention. Nucleic acids atleast 90%, more preferably 95%, and most preferably at least about98-99% identical with a nucleic sequence represented in one of SEQ IDNos: 1-4 are of course also within the scope of the invention. Inpreferred embodiments, the nucleic acid is mammalian. In comparing a newnucleic acid with known sequences, several alignment tools areavailable. Examples include PileUp, which creates a multiple sequencealignment, and is described in Feng et al., J. Mol. Evol. (1987)25:351-360. Another method, GAP, uses the alignment method of Needlemanet al., J. Mol. Biol. (1970) 48:443-453. GAP is best suited for globalalignment of sequences. A third method, BestFit, functions by insertinggaps to maximize the number of matches using the local homologyalgorithm of Smith and Waterman, Adv. Appl. Math. (1981) 2:482-489.

“Homology” and “identity” each refer to sequence similarity between twopolypeptide sequences, with identity being a more strict comparison.Homology and identity can each be determined by comparing a position ineach sequence which may be aligned for purposes of comparison. When aposition in the compared sequence is occupied by the same amino acidresidue, then the polypeptides can be referred to as identical at thatposition; when the equivalent site is occupied by the same amino acid(e.g., identical) or a similar amino acid (e.g., similar in stericand/or electronic nature), then the molecules can be referred to ashomologous at that position. A percentage of homology or identitybetween sequences is a function of the number of matching or homologouspositions shared by the sequences. An “unrelated” or “non-homologous”sequence shares less than 40 percent identity, though preferably lessthan 25 percent identity, with an HDx sequence of the present invention.

As used herein, an “HDx-related protein” refers to the HDx proteinsdescribed herein, and other human homologs of those HDx sequences, aswell as orthologs and paralogs (homologs) of the HDx proteins in otherspecies, ranging from yeast to other mammals, e.g., homologous histonedeacetylase. The term “ortholog” refers to genes or proteins which arehomologs via speciation, e.g., closely related and assumed to havecommon descent based on structural and functional considerations.Orthologous proteins function as recognizably the same activity indifferent species. The term “paralog” refers to genes or proteins whichare homologs via gene duplication, e.g., duplicated variants of a genewithin a genome. See also, Fritch, W M (1970) Syst Zool 19: 99-113.

“Cells”, “host cells”, or “recombinant host cells” are terms usedinterchangeably herein. It is understood that such terms refer not onlyto the particular subject cell but to the progeny or potential progenyof such a cell. Because certain modifications may occur in succeedinggenerations due to either mutation or environmental influences, suchprogeny may not, in fact, be identical to the parent cell, but are stillincluded within the scope of the term as used herein.

A “chimeric protein” or “fusion protein” is a fusion of a first aminoacid sequence encoding one of the subject HDx polypeptides with a secondamino acid sequence defining a domain (e.g. polypeptide portion) foreignto and not substantially homologous with any domain of one of the HDxproteins. A chimeric protein may present a foreign domain which is found(albeit in a different protein) in an organism which also expresses thefirst protein, or it may be an “interspecies”, “intergenic”, etc. fusionof protein structures expressed by different kinds of organisms. Ingeneral, a fusion protein can be represented by the general formulaX-HDx-Y, wherein HDx represents a portion of the protein which isderived from one of the HDx proteins, and X and Y are, independently,absent or represent amino acid sequences which are not related to one ofthe HDx sequences in an organism.

The term “isolated” as also used herein with respect to nucleic acids,such as DNA or RNA refers to molecules separated from other DNAs, orRNAs, respectively, that are present in the natural source of themacromolecule. For example, an isolated nucleic acid encoding one of thesubject HDx polypeptides preferably includes no more than 10 kilobases(kb) of nucleic acid sequence which naturally immediately flanks the HDxgene in genomic DNA, more preferably no more than 5 kb of such naturallyoccurring flanking sequences, and most preferably less than 1.5 kb ofsuch naturally occurring flanking sequence. The term isolated as usedherein also refers to a nucleic acid or peptide that is substantiallyfree of cellular material, viral material, or culture medium whenproduced by recombinant DNA techniques, or chemical precursors or otherchemicals when chemically synthesized. Moreover, an “isolated nucleicacid” is meant to include nucleic acid fragments which are not naturallyoccurring as fragments and would not be found in the natural state.

DETAILED DESCRIPTION OF THE INVENTION

The positioning of nucleosomes relative to particular regulatoryelements in genomic DNA has emerged as a mechanism for managing theassociation of sequence specific DNA-binding proteins with promoters,enhancers and other transcriptional regulatory sequences. Twomodifications to nucleosomes have been observed to influence theassociation of DNA-binding proteins with chromatin. Depletion ofhistones H2A/H2B from the nucleosome facilitates the binding of RNApolymerase II (Baer et al. (1983) Nature 301: 482-488) and TFIIIA (Hayeset al. (1992) PNAS 89:1229-1233). Likewise, acetylation of the corehistones apparently destabilizes the nucleosome and is thought tomodulate the accessibility of transcription factors to their respectiveenhancer and promoter elements (Oliva et al. (1990) Nuc. Acid Res. 18:2739-2747; and Walker et al. (1990) J. Biol. Chem. 265: 5622-5746). Inboth cases, overall histone-DNA contacts are altered.

In one aspect, the present invention concerns the discovery of new classof histone deacetylase genes in mammals, the gene products of which arereferred to herein as “histone deacetylases” or HDx's. Experimentalevidence indicates a functional role for the HDx gene products ascatalysts of the deacetylation of histones in mammalian cells, andaccordingly play a role in determining tissue fate and maintenance. Inaddition, however, other experimental evidence indicates a role that isbiochemically distinct from other classes of HDAC (class I), wherebyregulation of cellular localization is involved in the control of thetranscriptional activity of HDAC proteins.

The new class of histone deacetylase genes encode at least threedifferent sub-families, e.g., paralogs, and have been identified fromthe cells of various mammals. The HDx gene products described herein arereferred to as HD4, HD5 and HD6, and are represented in SEQ ID No.'s1-10.

As described below, one aspect of the invention pertains to isolatednucleic acids comprising nucleotide sequences encoding HDx polypeptides,and/or equivalents of such nucleic acids. The term nucleic acid as usedherein is intended to include fragments as equivalents. The termequivalent is understood to include nucleotide sequences encodingfunctionally equivalent HDx polypeptides or functionally equivalentpeptides having an activity of an HDx protein such as described herein.Equivalent nucleotide sequences will include sequences that differ byone or more nucleotide substitutions, additions, or deletions, such asallelic variants; and will, therefore, include sequences that differfrom the nucleotide sequence of the HDx cDNA sequences shown in any ofSEQ ID Nos: 1, 3 or 5, due to the degeneracy of the genetic code.Equivalents will also include nucleotide sequences that hybridize understringent conditions (i.e., equivalent to about 20-27° C. below themelting temperature (TM) of the DNA duplex formed in about 1M salt) tothe nucleotide sequences represented in one or more of SEQ ID Nos: 1, 3,or 5.

Moreover, it will be generally appreciated that, under certaincircumstances, it may be advantageous to provide homologs of one of thesubject HDx polypeptides which function in a limited capacity as one ofeither an HDx agonist (mimetic) or an HDx antagonist, in order topromote or inhibit only a subset of the biological activities of thenaturally occurring form of the protein. Thus, specific biologicaleffects can be elicited by treatment with a homolog of limited function,and with fewer side effects relative to treatment with agonists orantagonists which are directed to all of the biological activities ofnaturally occurring forms of HDx proteins.

Homologs of the subject HDx proteins can be generated by mutagenesis,such as by discrete point mutation(s), or by truncation. For instance,mutation can give rise to homologs which retain substantially the same,or merely a subset, of the biological activity of the HDx polypeptidefrom which it was derived. Alternatively, antagonistic forms of theprotein can be generated which are able to inhibit the function of thenaturally occurring form of the protein, as for example competing withwild-type HDx in the binding of a 14-3-3 protein, a MEF2 transcriptionfactor, RbAp48 or a histone. In addition, agonistic forms of the proteinmay be generated which are constitutively active, or have an alteredK_(cat) or K_(m) for deacetylation reactions. Thus, the HDx protein andhomologs thereof provided by the subject invention may be eitherpositive or negative regulators of transcription and/or activation.

In general, polypeptides referred to herein as having an activity of anHDx protein (e.g., are “bioactive”) are defined as polypeptides whichinclude an amino acid sequence corresponding (e.g., identical orhomologous) to all or a portion of the amino acid sequences of an HDxprotein shown in any one or more of SEQ ID Nos. 2, 4, 6, 7, 8, 9 or 10,which mimic or antagonize all or a portion of the biological/biochemicalactivities of a naturally occurring HDx protein. Examples of suchbiological activity include the ability to modulate proliferation ofcells. For example, inhibiting histone deacetylation causes cells toarrest in G1 and G2 phases of the cell cycle. The biochemical activityassociated with HDx proteins of the present invention can also becharacterized in terms of binding to and (optionally) catalyzing thedeacetylation of an acetylated histone.

Other biological activities of the subject new class of HDx proteins aredescribed herein or will be reasonably apparent to those skilled in theart. According to the present invention, a polypeptide has biologicalactivity if it is a specific agonist or antagonist of a naturallyoccurring form of an HDx protein.

A. Exemplary Nucleic Acids

Analysis of the new class of HDx sequences indicated similarity with theoriginal class of HDx (HD1) and x conserved residues are found. This,along with other experimental data suggests a role in the new class ofhuman HDx genes in the deacetylation of histones in mammalian cells. Inaddition, however, the new class of HDx proteins each contains a noveland conserved catalytic region represented by the consensus sequence:

(SEQ ID No.: 7) HHAXXXXXXGXCXFNXVAXXAXXXQXXXXXXXXXXLIVDWDXHHGXGTQXXFXXDPSVLYXSXHRYXXGXFXPXXWith reference to HD4, this catalytic region corresponds to amino acidresidues 802-874 of SEQ ID No. 2; with reference to HD5, this catalyticregion corresponds to amino acid residues 832-905 of SEQ ID No. 4; andwith respect to HD6, this catalytic region corresponds to two catalyticregions corresponding to amino acid residues 215-287 and amino acidresidues 610-683 of SEQ ID No. 6.

In another aspect, the invention provides a method of inhibiting a classII HDx. The method comprises contacting the HDx with a compound capableof initiating HDx activity, under conditions such that HDx activity isinhibited.

In another aspect, the invention provides a method of purifying an HDx.The method includes contacting a reaction mixture comprising an HDx withan affinity matrix capable of selectively binding to an HDx, andseparating at least one other component of the reaction mixture from theHDx.

Another aspect of the present invention relates to a method of inducingand/or maintaining a differentiated state, enhancing survival, and/orinhibiting (or alternatively potentiating) proliferation of a cell, bycontacting the cells with an agent which modulates HDx-dependenttranscription. For instance, it is contemplated by the invention that,in light of the present finding of an apparently broad involvement ofHDx proteins in the control of chromating structure and, thus,transcription and replication, the subject method could be used togenerate and/or maintain an array of different tissue both in vitro andin vivo. An “HDx therapeutic”, whether inhibitory or potentiating withrespect to modulating histone deacetylation, can be, as appropriate, anyof the preparations described above, including isolated polypeptides,gene therapy constructs, antisense molecules, peptidomimetics or agentsidentified in the drug assays provided herein.

In a further embodiment of the invention, the subject HDx therapeuticswill be useful in increasing the amount of protein produced by a cell orrecombinant cell. The cell may include any primary cell isolated fromany animal, cultured cells, immortalized cells, and established celllines. The animal cells used in the present invention include cellswhich intrinsically have an ability to produce a desired protein; cellswhich are induced to have an ability to produce a desired protein, forexample, by stimulation with a cytokine such as an interferon, aninterleukin; genetically engineered cells into which a gene for adesired protein is introduced. The protein produced by the process couldinclude any peptides or proteins, including peptide hormone orproteinaceous hormones such as any useful hormone, cytokine,interleukin, or protein which it may be desirable to have in purifiedform and/or in large quantity.

Another aspect of the invention features transgenic non-human animalswhich express a heterologous HDx gene of the present invention, or whichhave had one or more genomic HDx genes disrupted in at least one of thetissue or cell-types of the animal. Accordingly, the invention featuresan animal model for developmental diseases, which animal has one or moreHDx allele which is mis-expressed. For example, a mouse can be bredwhich has one or more HDx alleles deleted or otherwise renderedinactive. Such a mouse model can then be used to study disorders arising from mis-expressed HDx genes, as well as for evaluating potentialtherapies for similar disorders.

Another aspect of the present invention concerns transgenic animalswhich are comprised of cells (of that animal) which contain a transgeneof the present invention and which preferably (though optionally)express an exogenous HDx protein in one or more cells in the animal. AnHDx transgene can encode the wild-type form of the protein, or canencode homologs thereof, including both agonists and antagonists, aswell as antisense constructs. In preferred embodiments, the expressionof the transgene is restricted to specific subsets of cells, tissues ordevelopmental stages utilizing, for example, cis-acting sequences thatcontrol expression in the desired pattern. In the present invention,such mosaic expression of an HDx protein can be essential for many formsof lineage analysis and can additionally provide a means to assess theeffects of, for example, lack of HDx expression which might grosslyalter development in small patches of tissue within an otherwise normalembryo. Toward this end, tissue-specific regulatory sequences andconditional regulatory sequences can be used to control expression ofthe transgene in certain spatial patterns. Moreover, temporal patternsof expression can be provided by, for example, conditional recombinationsystems of prokaryotic transcriptional regulatory sequences.

Genetic techniques which allow for the expression of transgenes can beregulated via site-specific genetic manipulation in vivo are know tothose skilled in the art. For instance, genetic systems are availablewhich allow for the regulated expression of a recombinase that catalyzesthe genetic recombination a target sequence. As used herein, the phrase“target sequence” refers to a nucleotide sequence that is geneticallyrecombined by a recombinase. The target sequence is flanked byrecombinase recognition sequences and is generally either excised orinverted in cells expressing recombinase activity. Recombinase catalyzedrecombination events can be designed such that recombination of thetarget sequence results in either the activation or repression ofexpression of one of the subject HDx proteins. For example, excision ofa target sequence which interferes with the expression of a recombinantHDx gene, such as one which encodes an antagonistic homolog or anantisense transcript, can be designed to activate expression of thatgene. This interference with expression of the protein can result from avariety of mechanisms, such as spatial separation of the HDx gene fromthe promoter element or an internal stop codon. Moreover, the transgenecan be made wherein the coding sequence of the gene is flanked byrecombinase recognition sequences and is initially transfected intocells in a 3′ to 5′ orientation with respect to the promoter element. Insuch an instance, inversion of the target sequence will reorient thesubject gene by placing the 5′ end of the coding sequence in anorientation with respect to the promoter element which allows forpromoter driven transcriptional activation.

Similar conditional transgenes can be provided using prokaryoticpromoter sequences which require prokayrotic proteins to besimulataneously expressed in order to facilitate expression of the HDxtransgene. Exemplary promoters and the corresponding transactivatingprokaryotic proteins are given in U.S. Pat. No. 4,833,080.

Moreover, expression of the conditional transgenes can be induced bygene therapy-like methods wherein a gene encoding the trans-activatingprotein, e.g., a recombinase or a prokaryotic protein, is delivered tothe tissue and caused to be expressed, such as in a cell-type specificmanner. By this method, an HDx transgene could remain silent intoadulthood until “turned on” by the introduction of the transactivator.

In an exemplary embodiment, the “transgenic non-human animals” of theinvention are produced by introducing transgenes into the germline ofthe non-human animal. Embryic target cells at various developmentalstages can be used to introduce transgenes. Different methods are useddepending on the stage of development of the embryonic target cell. Thezygote is the best target for micro-injection. In the mouse, the malepronucleus reaches the size of approximately 20 micrometers in diameterwhich allows reproducible injection of 1-2 pl of DNA solution. The useof zygotes as a target for gene transfer has a major advantage in thatin most cases the injected DNA will be incorporated into the host genebefore the first cleavage (Brinster et al. (1985) PNAS 82:4438-4442). Asa consequence, all cells of the transgenic non-human animal will carrythe incorporated transgene. This will in general also be reflected inthe efficient transmission of the transgene to offspring of the foundersince 50% of the germ cells will harbor the transgene. Microinjection ofzygotes is the preferred method for incorporating transgenes inpracticing the invention.

Retroviral infection can also be used to introduce HDx transgenes into anon-human animal. The developing non-human embryo can be cultured invitro to the blastocyst stage. During this time, the blastomeres can betargets for retroviral infection (Jaenich, R. (1976) PNAS 73:1260-1264).Efficient infection of the blastomeres is obtained by enzymatictreatment to remove the zona pellucida (Manipulating the Mouse Embryo,Hogan eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor,1986). The viral vector system used to introduce the transgene istypically a replication-defective retrovirus carrying the transgene(Jahner et al. (1985) PNAS 82:6927-6931; Van der Putten et al. (1985)PNAS 82:6148-6152). Transfection is easily and efficiently obtained byculturing the blastomeres on a monolayer of virus-producing cells (Vander Putten, supra; Stewart et al. (1987) EMBO J. 6: 383-388).Alternatively, infection can be performed at a later stage. Virus orvirus-producing cells can be injected into the blastocoele (Jahner etal. (1982) Nature 298: 623-628). Most of the founders will be mosaic forthe transgene since incorporation occurs only in a subset of the cellswhich formed the transgenic non-human animal. Further, the founder maycontain various retrovial insertions of the transgene at differentpositions in the genome which generally will segregate in the offspring.In addition, it is also possible to introduce transgenes into the germline by intrauterine retroviral infection of the midgestation embryo(Jahner et al. (1982) supra).

A third type of target cell for transgene introduction is the embryonicstem cell (ES). ES cells are obtained from pre-implantation embryoscultured in vitro and fused with embryos (Evans et al (1981) Nature 292:154-156; Bradley et al. (1984) Nature 309: 255-258; Gossler et al.(1986) PNAS 83: 9065-9069; and Robertson et al (1986) Nature 322:445-448). Transgenes can be efficiently introduced into the ES cells byDNA transfection or by retrovirus-mediated transduction. Suchtransformed ES cells can thereafter be combined with blastocysts from anon-human animal. The ES cells thereafter colonize the embryo andcontribute to the germ line of the resulting chimeric animal. For reviewsee Jaenisch, R. (1988) Science 240: 1468-1474.

Methods of making HDx knock-out of disruption transgenic animals arealso generally known. See, for example, Manipulating the Mouse Embryo,(Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).Recombinase dependent knockouts can also be generated, e.g., byhomologous recombination to insert recombinase target sequences flankingportions of an endogenous HDx gene, such that tissue specific and/ortemporal control of inactivation of an HDx allele can be controlled asabove.

B. Exemplary Polypeptides

The present invention makes available isolated HDx polypeptides whichare isolated from, or otherwise substantially free of other cellularproteins. The term “substantially free of other cellular proteins” (alsoreferred to herein as “contaminating proteins”) or “substantially pureor purified preparations” are defined as encompassing preparations ofHDx polypeptides having less than about 20% (by dry weight)contaminating protein, and preferably having less than about 5%contaminating protein. Functional forms of the subject polypeptides canbe prepared, for the first time, as purified preparations by using acloned gene as described herein.

Preferred HDx proteins of the invention have an amino acid sequencewhich is at least about 60%, 70%, 80%, 85%, 90%, or 95% identical orhomologous to an amino acid sequence of any one of SEQ ID Nos. 1, 3 or5. Even more preferred HDx proteins comprise an amino acid sequencewhich is at least about 97, 98, or 99% homologous or identical to anamino acid sequence of any one of SEQ ID Nos. 1, 3, or 5. Such proteinscan be recombinant proteins, and can be, e.g., produced in vitro fromnucleic acids comprising a nucleotide sequence set forth in SEQ ID Nos.1, 3, or 5, or homologs thereof. For example, recombinant polypeptidespreferred by the present invention can be encoded by a nucleic acid,which is at least 85% homologous and more preferably 90% homologous andmost preferably 95% homologous with a nucleotide sequence set forth inSEQ ID NOS. 1, 3 or 5. Polypeptides which are encoded by a nucleic acidthat is at least about 98-99% homologous with the sequence of SEQ IDNOS: 1, 3 or 5 are also within the scope of the invention.

In a preferred embodiment, an HDx protein of the present invention is amammalian HDx protein, and more preferably a human HDx protein. In aparticularly preferred embodiment an HDx protein is set forth as SEQ IDNo: 2, 4 or 6. In particularly preferred embodiment, an HDx protein hasan HDx bioactivity. It will be understood that certainpost-translational modifications, e.g., phosphorylation and the like,can increase the apparent molecular weight of the HDx protein relativeto the unmodified polypeptide chain.

HDx polypeptides preferably are capable of functioning in one of eitherrole of an agonist or antagonist of at least one biological activity ofa wild-type (“authentic”) HDx protein of the appended sequence listing.The term “evolutionarily related to”, with respect to amino acidsequences of HDx proteins, refers to both polypeptides having amino acidsequences which have arisen naturally, and also to mutational variantsof human HDx polypeptides which are derived, for example, bycombinatorial mutagenesis. Full length proteins or fragmentscorresponding to one or more particular motifs and/or domains or toarbitrary sizes, for example, at least 5, 10, 25, 50, 75 and 100, aminoacids in length are within the scope of the present invention.

For example, isolated HDx polypeptides can be encoded by all or aportion of a nucleic acid sequence shown in any of SEQ ID NOS. 1, 3 or5. Isolated peptidyl portions of HDx proteins can be obtained byscreening peptides recombinantly produced from the correspondingfragment of the nucleic acid encoding such peptides. In addition,fragments can be chemically synthesized using techniques known in theart such as conventional Merrifield solid phase f-Moc or t-Bocchemistry. For example, an HDx polypeptide of the present invention maybe arbitrarily divided into fragments of desired length with no overlapof the fragments, or preferably divided into overlapping fragments of adesired length. The fragments can be produced (recombinantly or bychemical synthesis) and tested to identify those peptidyl fragmentswhich can function as either agonists or antagonists of a wild-type(e.g., “authentic”) HDx protein.

In general, polypeptides referred to herein as having an activity (e.g.,are “bioactive”) of an HDx protein are defined as polypeptides whichinclude an amino acid sequence encoded by all or a portion of thenucleic acid sequences shown in one of SEQ ID NOS: 1, 3 or 5, and whichmimic or antagonize all or a portion of the biological/biochemicalactivities of a naturally occurring HDx protein. Examples of suchbiological activity include the ability to deacetylate histones, bind tohistone(s), 14-3-3 proteins, MEF2 transcription factors and/or RbAp48.Other biological activities of the subject HDx proteins are describedherein or will be reasonably apparent to those skilled in the art.According to the present invention, a polypeptide has biologicalactivity if it is a specific agonist or antagonist of anaturally-occurring form of an HDx protein.

Other preferred proteins of the invention are those encoded by thenucleic acids set forth in the section pertaining to nucleic acids ofthe invention. In particular, the invention provides fusion proteins,e.g., HDx-immunoglobulin fusion proteins. Such fusion proteins canprovide, e.g., enhanced stability and solubility of HDx proteins and maythus be useful in therapy.

In addition to utilizing fusion proteins to enhance immunogenicity, itis widely appreciated that fusion proteins can also facilitate theexpression of proteins, and accordingly, can be used in the expressionof the HDx polypeptides of the present invention. For example, HDxpolypeptides can be generated as glutathione-S-transferase (GST-fusion)proteins. Such GST-fusion proteins can enable easy purification of theHDx polypeptide, as for example by the use of glutathione-derivatizedmatrices (see, for example, Current Protocols in Molecular Biology, eds.Ausubel et al. (N.Y.: John Wiley & Sons, 1991)).

The present invention further pertains to methods of producing thesubject HDx polypeptides. For example, a host cell transfected with anucleic acid vector directing expression of a nucleotide sequenceencoding the subject polypeptides can be cultured under appropriateconditions to allow expression of the peptide to occur. Suitable mediafor cell culture are well known in the art. The recombinant HDxpolypeptide can be isolated from cell culture medium, host cells, orboth using techniques known in the art for purifying proteins includingion-exchange chromatography, gel filtration chromatography,ultrafiltration, electrophoresis, and immunoaffinity purification withantibodies specific for such peptide. In a preferred embodiment, therecombinant HDX polypeptide is a fusion protein containing a domainwhich facilitates its purification, such as GST fusion protein.

Moreover, it will be generally appreciated that, under certaincircumstances, it may be advantageous to provide homologs of one of thesubject HDX polypeptides which function in a limited capacity as one ofeither an HDX agonist (mimetic) or an HDX antagonist, in order topromote or inhibit only a subset of the biological activities of thenaturally-occurring form of the protein. Thus, specific biologicaleffects can be elicited by treatment with a homolog of limited function,and with fewer side effects relative to treatment with agonists orantagonists which are directed to all of the biological activities ofnaturally occurring forms of HDX proteins.

Homologs of each of the subject HDX proteins can be generated bymutagenesis, such as by discrete point mutation(s), or by truncation.For instance, mutation can give rise to homologs which retainsubstantially the same, or merely a subset, of the biological activityof the HDX polypeptide from which it was derived. Alternatively,antagonistic forms of the protein can be generated which are able toinhibit the function of the naturally occurring form of the protein,such as by competitively binding to an HDX receptor.

The recombinant HDX polypeptides of the present invention also includehomologs of the wildtype HDX proteins, such as versions of those proteinwhich are resistant to proteolytic cleavage, as for example, due tomutations which alter ubiquitination or other enzymatic targetingassociated with the protein.

HDX polypeptides may also be chemically modified to create HDXderivatives by forming covalent or aggregate conjugates with otherchemical moieties, such as glycosyl groups, lipids, phosphate, acetylgroups and the like. Covalent derivatives of HDX proteins can beprepared by linking the chemical moieties to functional groups on aminoacid sidechains of the protein or at the N-terminus or at the C-terminusof the polypeptide.

Modification of the structure of the subject HDX polypeptides can be forsuch purposes as enhancing therapeutic or prophylactic efficacy,stability (e.g., ex vivo shelf life and resistance to proteolyticdegradation), or post-translational modifications (e.g., to alterphosphorylation pattern of protein). Such modified peptides, whendesigned to retain at least one activity of the naturally-occurring formof the protein, or to produce specific antagonists thereof, areconsidered functional equivalents of the HDX polypeptides described inmore detail herein. Such modified peptides can be produced, forinstance, by amino acid substitution, deletion, or addition. Thesubstitutional variant may be a substituted conserved amino acid or asubstituted non-conserved amino acid.

For example, it is reasonable to expect that an isolated replacement ofa leucine with an isoleucine or value, an aspartate with a glutamate, athreonine with a serine, or a similar replacement of an amino acid witha structurally related amino acid (i.e. isosteric and/or isoelectricmutations) will not have a major effect on the biological activity ofthe resulting molecule. Conservative replacements are those that takeplace within a family of amino acids that are related in their sidechains. Genetically encoded amino acids can be divided into fourfamilies: (1) acidic=aspartate, glutamate; (2) basic=lysine, arginine,histidine; (3) nonpolar=alanine, valine, leucine, isoleucine, proline,phenylalanine, methionine, tryptophan; and (4) uncharged polar=glycine,asparagine, glutamine, cysteine, serine, threonine, tyrosine. In similarfashion, the amino acid repertoire can be grouped as (1)acidic=aspartate, glutamate; (2) basic=lysine, arginine histidine, (3) aliphatic=glycine, alanine, valine, leucine, isoleucine, serine,threonine, with serine and threonine optionally be grouped separately asaliphatic-hydroxyl; (4) aromatic=phenylalanine, tyrosine, tryptophan;(5) amide=asparagine, glutamine; and (6) sulfur-containing=cysteine andmethionine, (see, for example, Biochemistry, 2^(nd) ed., Ed. by L.Stryer, WH Freeman and Co.: 1981). Whether a change in the amino acidsequence of a peptide results in a functional HDX homolog (e.g.,functional in the sense that the resulting polypeptide mimics orantagonizes the wild-type form) can be readily determined by assessingthe ability of the variant peptide to produce a response in cells in afashion similar to the wild-type protein, or competitively inhibit sucha response. Polypeptides in which more than one replacement has takenplace can readily be tested in the same manner.

This invention further contemplates a method for generating sets ofcombinatorial mutants of the subject HDX proteins as well as truncationmutants, and is especially useful for identifying potential variantsequences (e.g., homologs). The purpose of screening such combinatoriallibraries is to generate, for example, novel HDX homologs which can actas either agonists or antagonist, or alternatively, possess novelactivities all together. Thus, combinatorially-derived homologs can begenerated to have an increased potency relative to a naturally occurringform of the protein.

In one embodiment, the variegated library of HDX variants is generatedby combinatorial mutagenesis at the nucleic acid level, and is encodedby a variegated gene library. For instance, a mixture of syntheticoligonucleotides can be enzymatically ligated into gene sequences suchthat the degenerate set of potential HDX sequences are expressible asindividual polypeptides, or alternatively, as a set of larger fusionproteins (e.g., for phage display) containing the set of HDX sequencestherein.

There are many ways by which such libraries of potential HDX homologscan be generated from a degenerate oligonucleotide sequence. Chemicalsynthesis of a degenerate gene sequence can be carried out in anautomatic DNA synthesizer, and the synthetic genes then ligated into anappropriate expression vector. The purpose of a degenerate set of genesis to provide, in one mixture, all of the sequences encoding the desiredset of potential HDX sequences. The synthesis of degenerateoligonucleotides is well known in the art (see for example, Narang, S A(1983) Tetrahedron 39:3; Itakura et al. (1981) Recombinant DNA, Proc3^(rd) Cleveland Sympos. Macromolecules, ed. A G Walton, Amsterdam:Elsevier pp 273-289; Itakura et al. (1984) Annu. Rev. Biochem. 53:323;Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic AcidRes. 11:477. Such techniques have been employed in the directedevolution of other proteins (see, for example, Scott et al. (1990)Science 249:386-390; Roberts et al. (1992) PNAS 89:2429-2433; Devlin etal. (1990) Science 249: 404-406; Cwirla et al. (1990) PNAS 87:6378-6382; as well as U.S. Pat. Nos. 5,223,409, 5,198,346, and5,096,815).

Likewise, a library of coding sequence fragments can be provided for anHDX clone in order to generate a variegated population of HDX fragmentsfor screening and subsequent selection of bioactive fragments. A varietyof techniques are known in the art for generating such libraries,including chemical synthesis. In one embodiment, a library of codingsequence fragments can be generated by (i) treating a double strandedPCR fragment of an HDX coding sequence with a nuclease under conditionswherein nicking occurs only about once per molecule; (ii) denaturing thedouble stranded DNA; (iii) renaturing the DNA to form double strandedDNA which can include sense/antisense pairs from different nickedproducts; (iv) removing single stranded portions from reformed duplexesby treatment with S1 nuclease; and (v) ligating the resulting fragmentlibrary into an expression vector. By this exemplary method, anexpression library can be derived which codes for N-terminal, C-terminaland internal fragments of various sizes.

A wide range of techniques are known in the art for screening geneproducts of combinatorial libraries made by point mutations ortruncation, and for screening cDNA libraries for gene products having acertain property. Such techniques will be generally adaptable for rapidscreening of the gene libraries generated by the combinatorialmutagenesis of HDX homologs. The most widely used techniques forscreening large gene libraries typically comprises cloning the genelibrary into replicable expression vectors, transforming appropriatecells with the resulting library of vectors, and expressing thecombinatorial genes under conditions in which detection of a desiredactivity facilitates relatively easy isolation of the vector encodingthe gene whose product was detected. Each of the illustrative assaysdescribed below are amenable to high through-put analysis as necessaryto screen large numbers of degenerate HDX sequences created bycombinatorial mutagenesis techniques. Combinatorial mutagenesis has apotential to generate very large libraries of mutant proteins, e.g., inthe order of 10²⁶ molecules. Combinatorial libraries of this size may betechnically challenging to screen even with high throughput screeningassays. To overcome this problem, a new technique has been developedrecently, retrusive ensemble mutagenesis (REM), which allows one toavoid the very high proportion of non-functional proteins in a randomlibrary and simply enhances the frequency of functional proteins, thusdecreasing the complexity required to achieve a useful sampling ofsequence space. REM is an algorithm which enhances the frequency offunctional mutants in a library when an appropriate selection orscreening method is employed (Arkin and Yourvan, 1992, PNAS USA89:7811-7815; Yourvan et al., 1992, Parallel Problem Solving fromNature, 2. In Maenner and Manderick, eds., Elsevir Publishing Co.,Amsterdam, pp. 401-410; Delgrave et al., 1993, Protein Engineering6(3):327-331).

The invention also provides for reduction of the HDX proteins togenerate mimetics, e.g., peptide or non-peptide agents, such as smallmolecules, which are able to disrupt binding of an HDX polypeptide ofthe present invention with a molecule, e.g. target peptide. Thus, suchmutagenic techniques as described above are also useful to map thedeterminants of the HDX proteins which participate in protein-proteininteractions involved in, for example, binding of the subject HDXpolypeptide to a target peptide. To illustrate, the critical residues ofa subject HDX polypeptide which are involved in molecular recognition ofits receptor can be determined and used to generate HDX derivedpeptidomimetics or small molecules which competitively inhibit bindingof the authentic HDX protein with that moiety. By employing, forexample, scanning mutagenesis to map the amino acid residues of thesubject HDX proteins which are involved in binding other proteins,peptidomimetic compounds can be generated which mimic those residues ofthe HDX protein which facilitate the interaction. Such mimetics may thenbe used to interfere with the normal function of an HDX protein. Forinstance, non-hydrolyzable peptide analogs of such residues can begenerated using benzodiazepine (e.g., see Freidinger et al. in Peptides:Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden,Netherlands, 1988), azepine (e.g., see Huffman et al. in Peptides:Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden,Netherlands, 1988), substituted gamma lactam rings (Garvey et al. inPeptides: Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher:Leiden, Netherlands, 1988), keto-methylene pseudopeptides (Ewenson etal. (1986) J Med Chem 29:295; and Ewenson et al. in Peptides: Structureand Function (Proceedings of the 9^(th) American Peptide Symposium)Pierce Chemical Co. Rockland, Ill., 1985), b-turn dipeptide cores (Nagaiet al. (1985) Tetrahedron Lett 26:647; and Sato et al. (1986) J Chem SocPerkin Trans 1:1231), and b-aminoalcohols (Gordon et al. (1985) BiochemBiophys Res Commun 126:419; and Dann et al. (1986) Biochem Biophys ResCommun 134:71).

C. HDx Antibodies

Another aspect of the invention pertains to an antibody specificallyreactive with an HDx protein. For example, by using immunogens derivedfrom an HDx protein, e.g., based on the cDNA sequences,anti-protein/anti-peptide antisera or monoclonal antibodies can be madeby standard protocols (See, for example, Antibodies: A Laboratory Manualed. By Halow and Lane (Cold Spring Harbor Press: 1988)). A mammal, suchas a mouse, a hamster or rabbit can be immunized with an immunogenicform of the peptide (e.g., an HDx polypeptide or an antigenic fragmentwhich is capable of eliciting an antibody response). Techniques forconferring immunogenicity on a protein or peptide include conjugation tocarriers or other techniques well known in the art. An immunogenicportion of an HDx protein can be administered in the presence ofadjuvant. The progress of immunization can be monitored by detection ofantibody titers in plasma or serum. Standard ELISA or other immunoassayscan be used with the immunogen as antigen to assess the levels ofantibodies. In a preferred embodiment, the subject antibodies areimmunospecific for antigenic determinants of a class II HDx protein ofan organism, such as a mammal, e.g, antigenic determinants of a proteinrepresented by one of SEQ ID Nos, or closely related homologs (e.g., atleast 85% homologous, preferably at least 90% homologous, and morepreferably at least 90% identical). In yet a further embodiment of thepresent invention, in order to provide, for example, antibodies whichare immuno-selective for discrete HDx homologs, e.g, HDAC 4, HDAC5 orHDAC6, the anti-HDx polypeptide antibodies do not substantially crossreact (i.e., does not react specifically) with a protein which is, forexample, less than 85%, 90% or 95% homologous with the selected HDx. By“not substantially cross react”, it is meant that the antibody has abinding affinity for a non-homologous protein which is at least oneorder of magnitude, more preferably at least 2 orders of magnitude, andeven more preferably at least 3 orders of magnitude less than thebinding affinity of the antibody for the intended target HDx.

Following immunization of an animal with an antigenic preparation of anHDx polypeptide, anti-HDx antisera can be obtained and, if desired,polyclonal anti-HDx antibodies can be isolated from the serum. Toproduce monoclonal antibodies, antibody-producing cells (lymphocytes)can be harvested from an immunized animal and fused by standard somaticcell fusion procedures with immortalizing cells such as myeloma cells toyield hybridoma cells. Such techniques are well known in the art, andinclude, for example, the hybridoma technique (originally developed byKohler and Milstein, (1975) Nature, 256: 495-497), the human B cellhybridoma technique (Kozbar et al., (1983) Immunology Today, 4: 72), andthe EBV-hybridoma technique to produce human monoclonal antibodies (Coleet al., (1985) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss,Inc. pp. 77-96). Hybridoma cells can be screened immunochemically forproduction of antibodies specifically reactive with an HDx polypeptideof the present invention and monoclonal antibodies isolated from aculture comprising such hybridoma cells.

The term antibody, as used herein, is intended to include fragmentsthereof which are also specifically reactive with one of the subject HDxpolypeptides. Antibodies can be fragmented using conventional techniquesand the fragments screened for utility in the same manner as describedabove for whole antibodies. For example F(ab)2 fragments can begenerated by treating antibody with pepsin. The resulting F(ab)2fragment can be treated to reduce disulfide bridges to produce Fabfragments. The antibody of the present invention is further intended toinclude bispecific and chimeric molecules having affinity for an HDxprotein conferred by at least one CDR region of the antibody.

Both monoclonal and polyclonal antibodies (Ab) directed againstauthentic HDx polypeptides, or HDx variants, and antibody fragments suchas Fab, F(ab)₂, Fv and scFv can be used to block the action of one ormore HDx proteins and allow the study of the role of these proteins in,for example, differentiation of tissue. Experiments of this nature canaid in deciphering the role of HDx proteins that may be involved incontrol of proliferation versus differentiation, e.g., in patterning andtissue formation.

Antibodies which specifically bind HDx epitopes can also be used inimmunohistochemical staining of tissue samples in order to evaluate theabundance and pattern of expression of each of the subject HDxpolypeptides. Anti-HDx antibodies can be used diagnostically inimmuno-precipitation and immuno-blotting to detect and evaluate HDxprotein levels in tissue as part of a clinical testing procedure. Forinstance, such measurements can be useful in predictive valuations ofthe onset or progression of proliferative or differentiative disorders.Likewise, the ability to monitor HDx protein levels in an individual canallow determination of the efficacy of a given treatment regimen for anindividual affected with such a disorder. The level of HDx polypeptidesmay be measured from cells in bodily fluid, such as in samples ofcerebral spinal fluid or amniotic fluid, or can be measured in tissue,such as produced by biopsy. Diagnostic assays using anti-HDx antibodiescan include, for example, immunoassays designed to aid in earlydiagnosis of a disorder, particularly ones which are manifest at birth.Diagnostic assays using anti-HDx polypeptide antibodies can also includeimmunoassays designed to aid in early diagnosis and phenotypingneoplastic or hyperplastic disorders.

D. HDx Therapeutic Agents

As discussed above, purified and recombinant HDx polypeptides are madeavailable by the present invention and thus facilitates the developmentof assays which can be used to screen for drugs, including HDx homologs,which are either agonists of antagonists of the normal cellular functionof the subject HDx polypeptides, or of their role in the pathogenesis ofcellular differentiation and/or proliferation and disorders relatedthereto. In certain embodiments, the subject method is used to identifya gents which potentiate or inhibit the deacetylase activity of an HDxprotein. Moreover, because proteins have been identified which bind tothe subject HDx proteins, e.g., such as histones, 14-3-3 proteins, MEF2transcription factor, and RbAp48 as, the present invention furtherprovides drug screening assays for detecting agents which modulate thoseinteractions.

In a general sense, the assay evaluates the ability of a compound tomodulate binding between an HDx polypeptide and a molecule, be itprotein or DNA, that interacts with the HDx polypeptide, be it asubstrate of the deacetylase, or serves a regulatory function. Exemplarycompounds which can be screened include peptides, nucleic acids,carbohydrates, small organic molecules, and natural product extractlibraries, such as isolated from animals, plants, fungus and/ormicrobes.

It is contemplated that any of the novel interactions described hereincould be exploited in a drug screening assay. To illustrate, theinteraction between an HDx protein and a histone, a 14-3-3 protein orother HDx-binding protein can be detected in the presence and theabsence of a test compound. In other embodiments, the ability of acompound to modulate the acetylase activity of an HDx protein can beassessed. A variety of assay formats will suffice and, in light of thepresent inventions, will be comprehended by a skilled artisan.

In a preferred embodiment, assays which employ the subject mammalian HDxproteins can be used to identify compounds that have therapeutic indexesmore favorable than sodium butyrate, trapoxin, trichostatin or the like.For instance, trapoxin-like drugs can be identified by the presentinvention which have enhanced tissue-type or cell-type specificityrelative to trapoxin. To illustrate, the subject assays can be used togenerate compounds which preferentially inhibit IL-2 mediatedproliferation/activation of lymphocytes, or inhibit proliferation ofcertain tumor cells, without substantially interfering with othertissues, e.g. hepatocytes. Likewise, similar assays can be used toidentify drugs which inhibit proliferation of yeast cells or other lowereukaryotes, but which have a substantially reduced effect on mammaliancells, thereby improving therapeutic index of the drug as ananti-mycotic agent.

In one embodiment, the identification of such compounds is made possibleby the use of differential screening assays which detect and comparedrug-mediated inhibition of deacetylase activity or protein-protein orprotein-DNA interactions involving two or more different HDx enzymes,e.g., to find compounds that selectively inhibit class I or class I HDxproteins relative to one another or selectively inhibit one HDx proteinrelative to all the others. To illustrate, the assay can be designed forside-by-side comparison of the effect of a test compound on thedeacetylase activity or protein interactions of tissue-type specific HDxproteins. Given the apparent diversity of HDx proteins, it is probablethat different functional HDx activities, or HDx complexes exist and, incertain instances, are localized to particular tissue or cell types.Thus, test compounds can be screened for agents able to inhibit thetissue-specific formation of only a subset of the possible repertoire ofHDx/regulatory protein complexes, or which preferentially inhibitcertain HDx enzymes. In an exemplary embodiment, an interaction trapassay can be derived using class I and class II HDx “bait” proteins,while the “fish” protein is constant in each, e.g., a human RbAp48construct. Running the interaction trap side-by-side permits thedetection for agents which have a greater effect (e.g., statisticallysignificant) on the formation of one of the class I HDx/RbAp48 complexesthan on the formation of the class I HDx/RbAp48 complexes.

In similar fashion, differential screening assays can be used to exploitthe difference in protein interactions and/or catalytic mechanism ofmammalian HDx proteins and yeast RPD3 proteins in order to identifyagents which display a statistically significant increase in specificityfor inhibiting the yeast enzyme relative to the mammalian enzyme. Thus,lead compounds which act specifically on pathogens, such as fungusinvolved in mycotic infections, can be developed. By way ofillustration, the present assays can be used to screen for agents whichmay ultimately be useful for inhibiting at least one fungus implicatedin such mycosis as candidiasis, aspergillosis, mucormycosis,blastomycosis, geotrichosis, cryptococcosis, chromoblastomycosis,coccidioidomycosis, conidiosporosis, histoplasmosis, maduromycosis,rhinosporidosis, nocaidiosis, para-actinomycosis, penicilliosis,monoliasis, or sporotrichosis. For example, if the mycotic infection towhich treatment is desired is candidiasis, the present assay cancomprise comparing the relative effectiveness of a test compound oninhibiting the deacetylase activity of a mammalian HDx protein with itseffectiveness towards inhibiting the deacetylase activity of an RPD3homolog cloned from yeast selected from the group consisting of Candidaalbicans, Candida stellatoidea, Candida tropicalis, Candidaparapsilosis, Candida krusei, Candida pseudotropicalis, Candidaquillermondii, or Candida rugosa. Likewise, the present assay can beused to identify anti-fungal agents which may have therapeutic value inthe treatment of aspergillosis by selectively targeting RPD3 homologscloned from yeast such as Aspergillus fumigatus, Aspergillus flavus,Aspergillus niger, Aspergillus nidulans, or Aspergillus terreus. Wherethe mycotic infection is mucormycosis, the RPD3 deacetylase can bederived from yeast such as Rhizopus arrhizus, Rhizopus oryzae, Absidiacorymbifera, Absidia ramosa, or Mucor pusillus. Sources of other RPD3activities for comparison with a mammalian HDx activity includes thepathogen Pneumocystis carinii.

In addition to such HDx therapeutic uses, anti-fungal agents developedwith such differential screening assays can be used, for example, aspreservatives in foodstuff, feed supplement for promoting weight gain inlivestock, or in disinfectant formulations for treatment of non-livingmatter, e.g., for decontaminating hospital equipment and rooms.

In a similar fashion, side by side comparison of inhibition of mammalianHDx proteins and an insect HDx-related proteins, will permit selectionof HDx inhibitors which discriminate between the human/mammalian andinsect enzymes. Accordingly, the present invention expresslycontemplates the use and formulations of the subject HDx therapeutics ininsecticides, such as for use in management of insects like the fruitfly.

In yet another embodiment, certain of the subject HDx inhibitors can beselected on the basis of inhibitory specificity for plant HDx-relatedactivities relative to the mammalian enzyme. For example, a plantHDx-related protein can be disposed in a differential screen with one ormore of the human enzymes to select those compounds of greatestselectivity for inhibiting the plant enzyme. Thus, the present inventionspecifically contemplates formulations of the subject HDx inhibitors foragricultural applications, such as in the form of a defoliant or thelike.

In many drug screening programs which test libraries of compounds andnatural products, high throughput assays are desirable in order tomaximize the number of compounds surveyed in a given period of time.Assays which are performed in cell-free systems, such as may be derivedwith purified or semi-purified proteins, are often preferred as“primary” screens in that they can be generated to permit rapiddevelopment and relatively easy detection of an alteration in amolecular target which is mediated by a test compound. Moreover, theeffects of cellular toxicity and/or bioavailability of the test compoundcan be generally ignored in the in vitro system, the assay instead beingfocused primarily on the effect of the drug on the molecular target asmay be manifest in an alteration of binding affinity with upstream ordownstream elements. Accordingly, in an exemplary screening assay of thepresent invention, a reaction mixture is generated to include an HDxpolypeptide, compound(s) of interest, and a “target polypeptide” e.g., aprotein which interacts with the HDx polypeptide, whether as a substrateor by some other protein-protein interaction. Detection andquantification of complexes containing the HDx protein provide a meansfor determining a compound's efficacy at inhibiting (or potentiating)complex formation between the HDx and the target polypeptide. Theefficacy of the compound can be assessed by generating dose responsecurves from data obtained using various concentrations of the testcompound. Moreover, a control assay can also be performed to provide abaseline for comparison. In the control assay, isolate and purified HDxpolypeptide is added to a composition containing the target polypeptideand the formation of a complex is quantitated in the absence of the testcompound.

Complex formation between the HDx polypeptide and the target polypeptidemay be detected by a variety of techniques. Modulation of the formationof complexes can be quantitated using, for example, detectably labeledproteins such as radiolabeled, fluorescently labeled, or enzymaticallylabeled HDx polypeptides, by immunoassay, by chromatographic detection,or by detecting the intrinsic activity of the acetylase.

Typically, it will be desirable to immobilize either HDx or the targetpolypeptide to facilitate separation of complexes from uncomplexed formsof one or both of the proteins, as well as to accommodate automation ofthe assay. Binding of HDx to the target polypeptide, in the presence andabsence of a candidate agent, can be accomplished in any vessel suitablefor containing the reactants. Examples include microtitre plates, testtubes, and micro-centrifuge tubes. In one embodiment, a fusion proteincan be provided which adds a domain that allows the protein to be boundto the matrix. For example, glutathione-S-transferase/HDx (GST/HDx)fusion proteins can be adsorbed onto glutathione sepharose beads (SigmaChemical, St. Louis, Mo.) or glutathione derivatized microtitre plates,which are then combined with the cell lysates, e.g. an ³⁵S-labeled, andthe test compound, and the mixture incubated under conditions conduciveto complex formation, e.g. at physiological conditions for salt and pH,though slightly more stringent conditions may be desired. Followingincubation, the beads are washed to remove any unbound label, and thematrix immobilized and radiolabel determined directly (e.g. beads placedin scintillant), or in the supernatant after the complexes aresubsequently dissociated. Alternatively, the complexes can bedissociated from the matrix, separated by SDS-PAGE, and the level ofHDx-binding protein found in the bead fraction quantitated from the gelusing standard electrophoretic techniques such as described in theappended examples.

Other techniques for immobilizing proteins on matrices are alsoavailable for use in the subject assay. For instance, either HDx ortarget polypeptide can be immobilized utilizing conjugation of biotinand streptavidin. For instance, biotinylated HDx molecules can beprepared from biotin-NHS (N-hydroxy-succinimide) using techniques wellknown in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford,Ill.), and immobilized in the wells of streptavidin-coated 96 wellplates (Pierce Chemical). Alternatively, antibodies reactive with HDx,but which do not interfere with the interaction between the HDx andtarget polypeptide, can be derivatized to the wells of the plate, andHDx trapped in the wells by antibody conjugation. As above, preparationsof an target polypeptide and a test compound are incubated in theHDx-presenting wells of the plate, and the amount of complex trapped inthe well can be quantitated. Exemplary methods for detecting suchcomplexes, in addition to those described above for the GST-immobilizedcomplexes, include immunodetection of complexes using antibodiesreactive with the target polypeptide, or which are reactive with HDxprotein and compete with the target polypeptide; as well asenzyme-linked assays which rely on detecting an enzymatic activityassociated with the target polypeptide, either intrinsic or extrinsicactivity. In the instance of the latter, the enzyme can be chemicallyconjugated or provided as a fusion protein with the target polypeptide.To illustrate, the target polypeptide can be chemically cross-linked orgenetically fused with horseradish peroxidase, and the amount ofpolypeptide trapped in the complex can be assessed with a chromogenicsubstrate of the enzyme, e.g. 3,3′-diamino-benzadine terahydrochlorideor 4-chloro-1-napthol. Likewise, a fusion protein comprising thepolypeptide and glutathione-S-transferase can be provided, and complexformation quantitated by detecting the GST activity using1-chloro-2,4-dinitrobenzene (Habig et al (1974) J Biol Chem 249:7130).

For processes which rely on immunodetection for quantitating one of theproteins trapped in the complex, antibodies against the protein, such asanti-HDx antibodies, can be used. Alternatively, the protein to bedetected in the complex can be “epitope tagged” in the form of a fusionprotein which includes, in addition to the HDx sequence, a secondpolypeptide for which antibodies are readily available (e.g. fromcommercial sources). For instance, the GST fusion proteins describedabove can also be used for quantification of binding using antibodiesagainst the GST moiety. Other useful epitope tags include myc-epitopes(e.g., see Ellison et al. (1991) J Biol Chem 266:21150-21157) whichincludes a 10-residue sequence from c-myc, as well as the pFLAG system(International Biotechnologies, Inc.) or the pEZZ-protein A system(Pharmacia, NJ).

In another embodiment of a drug screening, a two hybrid assay can begenerated with an HDx and HDx-binding protein. Drug dependent inhibitionor potentiation of the interaction can be scored.

Where the HDx proteins themselves, or in complexes with other proteins,are capable of binding DNA and modifying transcription of a gene, atranscriptional based assay using, for example, an transcriptionalregulatory sequences responsive to HDx complexes operably linked to adetectable marker gene.

Furthermore, each of the assay systems set out above can be generated ina “differential” format as set forth above. That is, the assay formatcan provide information regarding specificity as well as potency. Forinstance, side-by-side comparison of a test compound's effect ondifferent HDxs can provide information on selectivity, and permit theidentification of compounds which selectively modulate the bioactivityof only a subset of the HDx family.

Furthermore, inhibitors of the enzymatic activity of each of the subjectHDx proteins can be identified using assays derived from measuring theability of an agent to inhibit catalytic conversion of a substrate bythe subject proteins. For example, the ability of the subject HDxproteins to deacetylate a histone substrate, such as histone H4, in thepresence and absence of a candidate inhibitor, can be determined usingstandard enzymatic assays.

A number of methods have been employed in the art for assaying histonedeacetylase activity, and can be incorporated in the drug screeningassays of the present invention. In preferred embodiments, the assaywill employ a labeled acetyl group linked to appropriate histone lysineresidues as substrates, in other embodiments, a histone substratepeptide can be labeled with a group whose signal is dependent on thesimultaneous presence or absence of an acetyl group, e.g., the label canbe a fluorogenic group whose fluorescence is modulated (either quenchedor potentiated) by the presence of the acetyl moiety. Using standardenzymatic analysis, the ability of a test agent to cause a statisticallysignificant change in substrate conversion by a histone deacetylase canbe measured, and as desirable, inhibition constants, e.g., K_(i) values,can be calculated. The histone substrate can be provided as a purifiedor semi-purified polypeptide or as part of a cell lysate. Likewise, thehistone deacetylase can be provided to the reaction mixture as apurified or semi-purified polypeptide or as a cell lysate. Accordingly,the reaction mixtures of the subject method can range from reconstitutedprotein mixtures derived with purified preparations of histones anddeacetylases, to mixtures of cell lysates, e.g., by admixing baculoviruslysates containing recombinant histones and deacetylases.

In an exemplary embodiment, the histone substrate for the subject assayis provided by isolation of radiolabeled histones from metabolicallylabelled cells. To illustrate, as described by Hay et al. (1983) J BiolChem 258:3726-3734, HeLa cells can be labelled in culture by addition of[³H]acetate (New England Nuclear) to the culture media. The addition ofbutyrate, trapoxin or the like can be used to increase the abundance ofacetylated histones in the cells. Radiolabelled histones can be isolatedfrom the cells by extraction with H_(s)SO₄ (Marushige et al. (1966) JMol Biol 15:160-174). Briefly, cells are homogenized in buffer,centrifuged to isolate a nuclear pellet, the subsequently homogenizednuclear pellet centrifuged through sucrose, and the resulting chromatinpellet extracted by addition of H_(s)SO₄ to yield [³H]acetyl-labelledhistones. In an alternate embodiment, nucleosome preparations containing[³H]acetyl-labelled histones can be isolated from the labelled cells. Asdescribed in the art, nucleosomes can be isolated from cell preparationsby sucrose gradient centrifugation (Hay et al. (1983) J Biol Chem258:3726-3734; and Noll (1967) Nature 215:360-363), and polynucleosomescan be prepared by NaCl precipitation from micrococcal nuclease digestedcells (Hay et al., supra). Similar procedures for isolating labelledhistones from other cells types, including yeast, have been described.See, for example, Alonso et al. (1986) Biochem Biophys Acta 866:161-169;and Kreiger et al. (1974) J Biol Chem 249:332-334. In yet otherembodiments, the histone is generated by recombinant gene expression,and includes an exogenous tag (e.g., an HA epitope, a poly(his) sequenceor the like) which facilitates in purification from cell extracts. Instill other embodiments, whole nuclei can be isolated from metabolicallylabelled cells by micrococcal nuclease digestion (Hay et al., supra)

In still another embodiment, the deacetylase substrate can be providedas an acetylated peptide including a sequence corresponding to thesequence about the specific lysyl residues acetylated on histone, e.g.,a peptidyl portions of the core histones H2A, H2B, H3 or H4. Suchfragments can be produced by cleavage of acetylated histones derivedfrom metabolically labelled cells, e.g., such as by treatment withproteolytic enzymes or cyanogen bromide (Kreiger et al., supra). Inother embodiments, the acetylated peptide can be provided by standardsolid phase synthesis using acetylated lysine residues (Kreiger et al.,supra).

Continuing with the illustrative use of [³H]acetyl-labelled histones,the activity of a histone deacetylase in the subject assays is detectedby measuring release of [³H]acetate by standard scintillant techniques.In a merely illustrative example, a reaction mixture is provided whichcomprises a recombinant HDx protein suspended in buffer, along with asample of [³H]acetyl-labelled histones and (optionally) a test compound.The reaction mixture is maintained at a desired temperature and pH, suchas 22° C. at pH7.8, for several hours, and the reaction terminated byboiling or other form of denaturation. Released [³H]acetate is extractedand counted. For example, the quenched reaction mixture can be acidifiedwith concentrated HCl, and used to create a biphasic mixture with ethylacetate. The resulting 2 phase system is thoroughly mixed, centrifuged,and the ethyl acetate phase collected and counted by standardscintillation methods. Other methods for detecting acetate release willbe easily recognized by those skilled in the art.

In yet another embodiment, the drug screening assay is derived toinclude a whole cell recombinantly expressing one or more of a targetprotein or HDx protein. The ability of a test agent to alter theactivity of the HDx protein can be detected by analysis of therecombinant cell. For example, agonists and antagonists of the HDxbiological activity can by detected by scoring for alterations in growthor differentiation (phenotype) of the cell. General techniques fordetecting each are well known, and will vary with respect to the sourceof the particular reagent cell utilized in any given assay.

For example, quantification of proliferation of cells in the presenceand absence of a candidate agent can be measured with a number oftechniques well known in the art, including simple measurement ofpopulation growth curves. For instance, where the assay involvesproliferation in a liquid medium, turbidimetric techniques (i.e.absorbence/transmittance of light of a given wavelength through thesample) can be utilized. For example, in the instance where the reagentcell is a yeast cell, measurement of absorbence of light at a wavelengthbetween 540 and 600 nm can provide a conveniently fast measure of cellgrowth. Likewise, ability to form colonies in solid medium (e.g. agar)can be used to readily score for proliferation. In other embodiments, anHDx substrate protein, such as a histone, can be provided as a fusionprotein which permits the substrate to be isolated from cell lysates andthe degree of acetylation detected. Each of these techniques aresuitable for high through-put analysis necessary for rapid screening oflarge numbers of candidate agents.

In addition, where the ability of an agent to cause or reverse atransformed phenotype, growth in solid media such as agar can furtheraid in establishing whether a mammalian cell is transformed.

Additionally, visual inspection of the morphology of the reagent cellcan be used to determine whether the biological activity of the targetedHDx protein has been affected by the added agent. To illustrate, theability of an agent to influence an apoptotic phenotype which ismediated in some way by a recombinant HDx protein can be assessed byvisual microscopy. Likewise, the formation of certain cellularstructures as part of differentiation, such as the formation of neuriticprocess, can be visualized under a light microscope.

The nature of the effect of test agent on reagent cell can be assessedby measuring levels of expression of specific genes, e.g., by reversetranscription-PCR. Another method of scoring for effect on Hdx activityis by detecting cell-type specific marker expression throughimmunofluorescent staining. Many such markers are known in the art, andantibodies are readily available. For example, the presence ofchondroitin sulphate proteoglycans as well as type-II collagen arecorrelated with cartilage production in chondrocytes, and each can bedetected by immunostaining. Similarly, the human kidney differentiationantigen gp160, human aminopeptidase A, is a marker of kidney induction,and the cytoskeletal protein troponin I is a marker of heart induction.In yet another embodiment, the alteration of expression of a reportergene construct provided in the reagent cell provides a means ofdetecting the effect on HDx activity. For example, reporter geneconstructs derived using the transcriptional regulatory sequences, e.g.the promoters, for developmentally regulated genes can be used to drivethe expression of a detectable marker, such as a luciferase gene. In anillustrative embodiment, the construct is derived using the promotersequence from a gene expressed in a particular differentiativephenotype.

It is also deemed to be within the scope of this invention that therecombinant HDx cells of the present assay can be generated so as tocomprise heterologous HDx proteins (i.e. cross-species expression). Forexample, HDx proteins from one species can be expressed in the cells ofanother under conditions wherein the heterologous protein is able torescue loss-of-function mutations in the host cell. For example, thereagent cell can be a yeast cell in which a human MDx protein (e.g.exogenously expressed) is the intended target for development of ananti-proliferative agent. To illustrate, the M778 strain, MATa ura3-52trp1□i his3-200 leu2-1 trk1□ rpd3::HIS3, described by Vidal et al.(1991) Mol Cell Biol 6317-6327, which lacks a functional endogenous RPD3gene can be transfected with an expression plasmid including a mammalianHDx gene in order to complement the RPD3 loss-of-function. For example,the coding sequence for HD4, HD5 or HD6 can be cloned into a pRSintegrative plasmid containing a selectable marker (Sikorski et al.(1989) Genetics 122:19-27), and resulting construct used to transformthe M778 strain. The resulting cells should produce a mammalian HDxprotein which may be capable performing at least some of the functionsof the yeast RPD3 protein. The HDx transformed yeast cells can be easierto manipulate than mammalian cells, and can provide access to certainassay formats, such as turbidity detection methods, which may not beobtainable with mammalian cells.

Moreover, the combination of the “mammalianized” strain with the strainM537 (MATa ura3-52 trp1□i his3-200 leu2-1 trk1□, Vidal et al., supra)can provide an exquisitely sensitive cell-based assay for detectingagent which specifically inhibit, for example, the yeast RPD3deacetylase.

E. Small Molecule Combinatorial Libraries for HDx Inhibitors

The subject reactions readily lend themselves to the creation ofcombinatorial libraries of compounds for the screening ofpharmaceutical, agrochemical or other biological or medically-relatedactivity or material-related qualities. A combinatorial library for thepurposes of the present invention is a mixture of chemically relatedcompounds which may be screened together for a desired property; saidlibraries may be in solution or covalently linked to a solid support.The preparation of many related compounds in a single reaction greatlyreduces and simplifies the number of screening processes which need tobe carried out. Screening for the appropriate biological,pharmaceutical, agrochemical or physical property may be done byconventional methods.

Diversity in a library can be created at a variety of different levels.For instance, the substrate aryl groups used in a combinatorial approachcan be diverse in terms of the core aryl moiety, e.g., a variegation interms of the ring structure, and/or can be varied with respect to theother substituents.

A variety of techniques are available in the art for generatingcombinatorial libraries of small organic molecules. See, for example,Blondelle et al. (1995) Trends Anal. Chem. 14:83; the Affymax U.S. Pat.Nos. 5,359,115 and 5,362,899: the Ellman U.S. Pat. No. 5,288,514: theStill et al. PCT publication WO 94/08051; Chen et al. (1994) JACS116:2661: Kerr et al. (1993) JACS 115:252; PCT publications WO92/10092,WO93/09668 and WO91/07087; and the Lerner et al. PCT publicationWO93/20242). Accordingly, a variety of libraries on the order of about16 to 1,000,000 or more diversomers can be synthesized and screened fora particular activity or property.

In an exemplary embodiment, a library of substituted diversomers can besynthesized using the subject reactions adapted to the techniquesdescribed in the Still et al. PCT publication WO 94/08051, e.g., beinglinked to a polymer bead by a hydrolyzable or photolyzable group, e.g.,located at one of the positions of substrate. According to the Still etal. technique, the library is synthesized on a set of beads, each beadincluding a set of tags identifying the particular diversomer on thatbead. In one embodiment, which is particularly suitable for discoveringenzyme inhibitors, the beads can be dispersed on the surface of apermeable membrane, and the diversomers released from the beads by lysisof the bead linker. The diversomer from each bead will diffuse acrossthe membrane to an assay zone, where it will interact with an enzymeassay. Detailed descriptions of a number of combinatorial methodologiesare provided below.

Direct Characterization

A growing trend in the field of combinatorial chemistry is to exploitthe sensitivity of techniques such as mass spectrometry (MS), e.g.,which can be used to characterize sub-femtomolar amounts of a compound,and to directly determine the chemical constitution of a compoundselected from a combinatorial library. For instance, where the libraryis provided on an insoluble support matrix, discrete populations ofcompounds can be first released from the support and characterized byMS. In other embodiments, as part of the MS sample preparationtechnique, such MS techniques as MALDI can be used to release a compoundfrom the matrix, particularly where a labile bond is used originally totether the compound to the matrix. For instance, a bead selected from alibrary can be irradiated in a MALDI step in order to release thediversomer from the matrix, and ionize the diversomer for MS analysis.

Multipin Synthesis

The libraries of the subject method can take the multipin libraryformat. Briefly, Geysen and co-workers (Geysen et al. (1984) PNAS81:3998-4002) introduced a method for generating compound libraries by aparallel synthesis on polyacrylic acid-grated polyethylene pins arrayedin the microtitre plate format. The Geysen technique can be used tosynthesize and screen thousands of compounds per week using the multipinmethod, and the tethered compounds may be reused in many assays.Appropriate linker moieties can also been appended to the pins so thatthe compounds may be cleaved from the supports after synthesis forassessment of purity and further evaluation (c.f., Bray et al. (1990)Tetrahedron Lett 31:5811-5814; Valerio et al. (1991) Anal Biochem197:168-177; Bray et al. (1991) Tetrahedron Lett 32:6163-6166).

Divide-Couple-Recombine

In yet another embodiment, a variegated library of compounds can beprovided on a set of beads utilizing the strategy ofdivide-couple-recombine (see, e.g., Houghten (1985) PNAS 82:5131-5135;and U.S. Pat. Nos. 4,631,211; 5,440,016; 5,480,971). Briefly, as thename implies, at each synthesis step where degeneracy is introduced intothe library, the beads are divided into separate groups equal to thenumber of different substituents to be added at a particular position inthe library, the different substituents coupled in separate reactions,and the beads recombined into one pool for the next iteration.

In one embodiment, the divide-couple-recombine strategy can be carriedout using an analogous approach to the so-called “tea bag” method firstdeveloped by Houghten, where compound synthesis occurs on resin sealedinside porous polypropylene bags (Houghten et al. (1986) PNAS82:5131-5135). Substituents are coupled to the compound-bearing resinsby placing the bags in appropriate reaction solutions, while all commonsteps such as resin washing and deprotection are performedsimultaneously in one reaction vessel. At the end of the synthesis, eachbag contains a single compound.

Combinatorial Libraries by Light-Directed, Spatially AddressableParallel Chemical Synthesis

A scheme of combinatorial synthesis in which the identity of a compoundis given by its locations on a synthesis substrate is termed aspatially-addressable synthesis. In one embodiment, the combinatorialprocess is carried out by controlling the addition of a chemical reagentto specific locations on a solid support (Dower et al. (1991) Annu RepMed Chem 26:271-280; Fodor, S. P. A. (1991) Science 251:767; Pirrung etal. (1992) U.S. Pat. No. 5,143,854; Jacobs et al. (1994) TrendsBiotechnol 12:19-26). The spatial resolution of photolithography affordsminiaturization. This technique can be carried out through the useprotection/deprotection reactions with photolabile protecting groups.

The key points of this technology are illustrated in Gallop et al.(1994) J Med Chem 37:1233-1251. A synthesis substrate is prepared forcoupling through the covalent attachment of photolabilenitroveratryloxycarbonyl (NVOC) protected amino linkers or otherphotolabile linkers. Light is used to selectively activate a specifiedregion of the synthesis support for coupling. Removal of the photolabileprotecting groups by light (deprotection) results in activation ofselected areas. After activation, the first of a set of amino acidanalogs, each bearing a photolabile protecting group on the aminoterminus, is exposed to the entire surface. Coupling only occurs inregions that were addressed by light in the preceding step. The reactionis stopped, the plates washed, and the substrate is again illuminatedthrough a second mask, activating a different region for reaction with asecond protected building block. The pattern of masks and the sequenceof reactants define the products and their locations. Since this processutilizes photolithography techniques, the number of compounds that canbe synthesized is limited only by the number of synthesis sites that canbe addressed with appropriate resolution. The position of each compoundis precisely known; hence, its interactions with other molecules can bedirectly assessed.

In a light-directed chemical synthesis, the products depend on thepattern of illumination and on the order of addition of reactants. Byvarying the lithographic patterns, many different sets of test compoundscan be synthesized simultaneously; this characteristic leads to thegeneration of many different masking strategies.

Encoded Combinatorial Libraries

In yet another embodiment, the subject method utilizes a compoundlibrary provided with an encoded tagging system. A recent improvement inthe identification of active compounds from combinatorial librariesemploys chemical indexing systems using tags that uniquely encode thereaction steps a given bead has undergone and, by inference, thestructure it carries. Conceptually, this approach mimics phage displaylibraries, where activity derives from expressed peptides, but thestructures of the active peptides are deduced from the correspondinggenomic DNA sequence. The first encoding of synthetic combinatoriallibraries employed DNA as the code. A variety of other forms of encodinghave been reported, including encoding with sequenceable bio-oligomers(e.g., oligonucleotides and peptides), and binary encoding withadditional non-sequenceable tags.

Tagging with Sequenceable Bio-Oligomers

The principle of using oligonucleotides to encode combinatorialsynthetic libraries was described in 1992 (Brenner et al. (1992) PNAS89:5381-5383), and an example of such a library appeared the followingyear (Needles et al. (1993) PNAS 90:10700-10704). A combinatoriallibrary of nominally 7⁷ (=823,543) peptides composed of all combinationsof Arg, Gln, Phe, Lys, Val, D-Val and Thr (three-letter amino acidcode), each of which was encoded by a specific dinucleotide (TA, TC, CT,AT, TT, CA and AC, respectively), was prepared by a series ofalternating rounds of peptide and oligonucleotide synthesis on solidsupport. In this work, the amine linking functionality on the bead wasspecifically differentiated toward peptide or oligonucleotide synthesisby simultaneously preincubating the beads with reagents that generateprotected OH groups for oligonucleotide synthesis and protected NH₂groups for peptide synthesis (here, in a ratio of 1:20). When complete,the tags each consisted of 69-mers, 14 units of which carried the code.The bead-bound library was incubated with a fluorescently labeledantibody, and beads containing bound antibody that fluoresced stronglywere harvested by fluorescence-activated cell sorting (FACS). The DNAtags were amplified by PCR and sequenced, and the predicted peptideswere synthesized. Following such techniques, compound libraries can bederived for use in the subject method, where the oligonucleotidesequence of the tag identifies the sequential combinatorial reactionsthat a particular bead underwent, and therefore provides the identity ofthe compound on the bead.

The use of oligonucleotide tags permits exquisitely sensitive taganalysis. Even so, the method requires careful choice of orthogonal setsof protecting groups required for alternating co-synthesis of the tagand the library member. Furthermore, the chemical lability of the tag,particularly the phosphate and sugar anomeric linkages, may limit thechoice of reagents and conditions that can be employed for the synthesisof non-oligomeric libraries. In preferred embodiments, the librariesemploy linkers permitting selective detachment of the test compoundlibrary member for assay.

Peptides have also been employed as tagging molecules for combinatoriallibraries. Two exemplary approaches are described in the art, both ofwhich employ branched linkers to solid phase upon which coding andligand strands are alternately elaborated. In the first approach (Kerr JM et al. (1993) J Am Chem Soc 115:2529-2531), orthogonality in synthesisis achieved by employing acid-labile protection for the coding strandand base-labile protection for the compound strand.

In an alternative approach (Nikolaiev et al. (1993) Pept Res 6:161-170),branched linkers are employed so that the coding unit and the testcompound can both be attached to the same functional group on the resin.In one embodiment, a cleavable linker can be placed between the branchpoint and the bead so that cleavage releases a molecule containing bothcode and the compound (Ptek et al. (1991) Tetrahedron Lett32:3891-3894). In another embodiment, the cleavable linker can be placedso that the test compound can be selectively separated from the bead,leaving the code behind. This last construct is particularly valuablebecause it permits screening of the test compound without potentialinterference of the coding groups. Examples in the art of independentcleavage and sequencing of peptide library members and theircorresponding tags has confirmed that the tags can accurately predictthe peptide structure.

Non-Sequenceable Tagging: Binary Encoding

An alternative form of encoding the test compound library employs a setof non-sequenceable electrophoric tagging molecules that are used as abinary code (Ohlmeyer et al. (1993) PNAS 90:10922-10926). Exemplary tagsare haloaromatic alkyl ethers that are detectable as theirtrimethylsilyl ethers at less than femtomolar levels by electron capturegas chromatography (ECGC). Variations in the length of the alkyl chain,as well as the nature and position of the aromatic halide substituents,permit the synthesis of at least 40 such tags, which in principle canencode 2⁴⁰ (e.g., upwards of 10¹²) different molecules. In the originalreport (Ohlmeyer et al., supra) the tags were bound to about 1% of theavailable amine groups of a peptide library via a photocleavableo-nitrobenzyl linker. This approach is convenient when preparingcombinatorial libraries of peptide-like or other amine-containingmolecules. A more versatile system has, however, been developed thatpermits encoding of essentially any combinatorial library. Here, thecompound would be attached to the solid support via the photocleavablelinker and the tag is attached through a catechol ether linker viacarbene insertion into the bead matrix (Nestler et al. (1994) J Org Chem59:4723-4724). This orthogonal attachment strategy permits the selectivedetachment of library members for assay in solution and subsequentdecoding by ECGC after oxidative detachment of the tag sets.

Although several amide-linked libraries in the art employ binaryencoding with the electrophoric tags attached to amine groups, attachingthese tags directly to the bead matrix provides far greater versatilityin the structures that can be prepared in encoded combinatoriallibraries. Attached in this way, the tags and their linker are nearly asunreactive as the bead matrix itself. Two binary-encoded combinatoriallibraries have been reported where the electrophoric tags are attacheddirectly to the solid phase (Ohlmeyer et al. (1995) PNAS 92:6027-6031)and provide guidance for generating the subject compound library. Bothlibraries were constructed using an orthogonal attachment strategy inwhich the library member was linked to the solid support by aphotolabile linker and the tags were attached through a linker cleavableonly by vigorous oxidation. Because the library members can berepetitively partially photoeluted from the solid support, librarymembers can be utilized in multiple assays. Successive photoelution alsopermits a very high throughput iterative screening strategy: first,multiple beads are placed in 96-well microtiter plates; second,compounds are partially detached and transferred to assay plates; third,a metal binding assay identifies the active wells; fourth, thecorresponding beads are rearrayed singly into new microtiter plates;fifth, single active compounds are identified; and sixth, the structuresare decoded.

Examples

The invention, now being generally described, will be more readilyunderstood by reference to the following examples, which are includedmerely for purposes of illustration of certain aspects and embodimentsof the present invention and are not intended to limit the invention.

Experimental Results A. Identification of Three Novel Class II humanHDAC Enzymes

The NCBI database was screened with the yeast Hda1p amino acid sequenceto identify human homologs. The complete ORFs of HDAC 4, 5, and 6 wereconstructed as described in Methods. HDAC4 consists of 1085 amino acids,with a putative catalytic region beginning at amino acid 802 (FIG. 1A).HDAC5 is highly homologous to HDAC4 (51% identity, 63% similarity), with1123 amino acids and a catalytic region beginning at amino acid 832(FIG. 1B). HDAC6 is the largest HDAC protein yet identified in humans,with 1216 amino acids. It is also unique in that it consists of anapparent internal dimer containing two catalytic domains, with the firstbeginning at amino acid 215 and the second at amino acid 610 (FIG. 1C).The two catalytic regions in HDAC6 are highly homologous to each other(47% identity, 64% similarity) and therefore the protein may have arisenevolutionarily from an in frame gene duplication event. All thecatalytic domains of these three proteins are highly conserved withrespect to each other and previously identified HDAC proteins (FIG. 1D).There are 15 invariant residues in this region between HDAC1, 4, 5, 6proteins and Hda1p, and a total of 37 invariant residues within the fourcatalytic domains of the three new HDAC proteins. This level of sequenceconservation strongly suggests that these novel proteins havedeacetylase activity.

B. Differential Expression of Class II HDACs in Human Tissues

Northern blot analyses indicate differential tissue expression of thehuman class II HDACs (FIG. 2). HDAC4 is detectable as a 9.6 kbtranscript in brain, heart and skeletal muscle tissues. The signal isvery weak, however, which may have been caused by the fact that thetranscript is at the upper size limit for mRNA samples in thisparticular blot. It is possible that HDAC4 is expressed in othertissues, but the quantity of transcript in these samples may be too lowto detect. This finding is consistent with the small number of ESTscorresponding to this cDNA present in the database. HDAC5 expressionpartially overlaps that of HDAC4, and is observed primarily in brain,heart, skeletal muscle, and placental tissues as a 3.7 kb transcript.HDAC6, which is present as a 5 kb transcript, has the highest expressionlevels in heart, liver, kidney, and pancreas. The differences in tissueexpression may reflect a tissue specific function of these enzymes.

C. In Vitro Histone Deacetylase Activity of Class II HDACs

To determine if HDAC4, 5 and 6 possess histone deacetylase activity, therecombinant proteins were assayed for enzymatic activity in vitro.Epitope-tagged recombinant HDACs 1, 4, 5, and 6 were expressed inTag-Jurkat cells and immunoprecipitated. The immunoprecipitates wereincubated with ³H-acetate labeled histones, and the subsequent releaseof ³H-acetate was quantified by scintillation counting. All four HDACenzymes exhibit deacetylation activity that is at least two-fold abovebackground levels (FIG. 3A). In each case, activity is greatly reducedby the presence of 300 nM TSA, a potent HDAC inhibitor. HDAC1 and HDAC6possess comparable activity, whereas that of HDAC4 and HDAC5 is somewhatreduced. This is most likely due to lower expression levels for thesetwo recombinant proteins rather than inherently weaker histonedeacetylase activity (see FIG. 5A). Furthermore, co-immunoprecipitationexperiments (see FIG. 5 b) demonstrate the association of HDAC4 andHDAC5 with HDAC3. It is possible that the observed HDAC activity is dueto HDAC3. However, sequence analysis suggests that HDAC4 and HDAC5possess functional catalytic domains, and therefore should contribute tothe activity. Therefore, in vitro, all three human class II HDACs candeacetylate histones in a trichostatin-sensitive manner.

Previously, Hda1p was shown to preferentially deacetylate histone H3 invitro (16). In order to determine if HDAC4, 5 and 6 display similarpreferences, the immunopurified recombinant proteins were incubated with³H-acetate labeled histones and the deacetylase reactions were separatedby SDS/PAGE to identify the different histone isotypes. The gel was thenexposed to autoradiography to determine the relative amount ofacetylated histones remaining in each case. HDAC1, 4, 5, and 6deacetylate all four core histories equally well, though againdeacetylation by HDAC4 and HDAC5 is incomplete (FIG. 3B).

D. Independently Active Catalytic Domains of HDAC6

HDAC6 possesses two separate putative catalytic domains. Site-directedmutagenesis was performed in order to determine if either domainrequired the other for catalytic activity. Histidine 141 of HDAC1 wasshown previously to be critical for deacetylase activity (18). Thecorresponding histidine residues in each catalytic domain of HDAC6 weremutated to alanine, to produce the H216A and H611A single mutants andthe H216/611A double mutant. The mutant HDAC6 proteins were expressedand assayed for in vitro deacetylation of histories. Mutation of eitherH216 or H611 to alanine results in a slight reduction of histonedeacetylase activity, and simultaneous mutation of both sites abrogatesthis activity completely (FIG. 4A, 4B). Furthermore, a truncation ofHDAC6 containing the N-terminal 460 amino acids, and therefore only thefirst catalytic domain, is still catalytically active (data not shown).Therefore, both catalytic domains of HDAC6 are fully functional histonedeacetylases and contribute independently to the overall activity of thewild-type HDAC6 protein.

E. Expression and Co-Immunoprecipitation of Class II HDACs

Recombinant, FLAG epitope-tagged proteins were subjected to Western blotanalysis to address possible protein-protein interactions. HDAC1migrates as a band slightly above its expected size of 55 kDa inSDS/PAGE (FIG. 5A). Recombinant HDAC4 and 6 appeared above theirtheoretical molecular weights of 119 kDa and 131 kDa, respectively. Theexpression level of HDAC5 is significantly lower than the others, andthe protein appears as a doublet, both in the lysate (data not shown)and in the immunoprecipitate (FIG. 5A). This doublet may be the resultof post-translational modifications or partial proteolytic degradation.The high molecular weight diffuse signal apparent in the blot is mostlikely due to cross-reaction of the secondary mouse antibody withcontaminating FLAG antibody used for the immunoprecipitation. Thissignal is partially masked by the comigration of the recombinant HDAC4,5 and 6 proteins.

HDAC1 has been shown to be associated with a variety oftranscription-related proteins, including the CHD chromodomain proteins,metastasis-associated factors (MTA), the co-repressor mSin3A and thehistone-binding protein RbAp48. In order to determine if HDAC4, 5, and 6associated with the same proteins in vivo, a series ofco-immunoprecipitation experiments was performed. Immunoprecipitateswere probed with □-CHD4, □-mSin3A, □-MTA, □-RbAp48, □-HDAC1, and □-HDAC3antibodies (FIG. 5B). The HDAC1 sample contains bands corresponding toall proteins with the exception of HDAC3, as anticipated. There is aband in the mSin3A blot of the HDAC4 immunoprecipitate, which appears ata lower molecular weight than expected for mSin3A. The nature of thisband is unclear, since it does not correspond to any of the previouslyobserved forms of mSin3A. HDAC4 coimmunoprecipitates with Rbp48 andHDAC3, though none of the other proteins were apparent. HDAC5 associatesonly with HDAC3, though it is possible that the expression levels weretoo low to detect other associated factors. HDAC6 does not appear tointeract with any of these proteins, despite robust expression, nor wasHDAC1 or HDAC2 found to co-immunoprecipitate with the class II HDACs.This analysis suggests that these novel class II HDAC proteins arebiochemically distinct from HDAC1 in vivo.

F. Immunoprecipitation of HDAC4 and HDAC5 Complexes

Recombinant, FLAG-epitope tagged HDAC1 and HDAC4 were transientlyexpressed in TAg Jurkat cells and immunoprecipitated with □-FLAGantibodies. The purified proteins were separated by SDS/PAGE andvisualized by silver staining. Comparison with the mock-transfectednegative control and the HDAC1 samples revealed the presence of specific30- and 32-kDa protein bands in the HDAC4 immunoprecipitate. Peptidesderived from these proteins were analyzed by peptide microsequencing andfound to correspond to the □ and □ isoforms of 14-3-3, respectively(FIG. 7A). Duo to the high degree of sequence similarity between HDAC4and HDAC5 (51% identity), it was hypothesized that HDAC5 associates with14-3-3 proteins as well. The presence of these two 14-3-3 proteinisoforms in both HDAC4 and HDAC5 immunoprecipitates was confirmed byWestern blot analysis with isoform-specific antibodies (FIG. 7B). Thisanalysis also confirmed the previously observed association of HDAC3with both class II HDACs. These immunoprecipitation experiments suggestthat HDAC4 and HDAC5 can associate, either directly or indirectly, bothwith HDAC3, which is nuclear (Emiliani et al., 1998), and 14-3-3proteins, which are generally cytoplasmic (Burbelo and Hall, 1995).

G. Nuclear-Cytoplasmic Shuttling of HDAC4 and HDAC5 is Regulated byBinding to 14-3-3

We and other groups (Miska et al., 1999) have observed byimmunofluorescence that HDAC4 and HDAC5 can be localized to either thecytoplasm or the nucleus, often aggregating in discrete foci (FIG. 8A).This nuclear and cytoplasmic localization is dynamic and shuttling canoccur under normal conditions of cell growth. Recombinant HDAC4-EGFP wastransiently expressed in COS-7 cells, and the localization of theprotein was monitored over a period of three hours in live cells. Whilethe localization of HDAC4-EGFP remained static in the majority of cells,shuttling was observed in some cases (data not shown). Thisnuclear-cytoplasmic shuttling process could explain the apparentdiscrepancy observed in the immunoprecipitation experiments, in whichHDAC4 and HDAC5 were found to interact with both nuclear HDAC3 andcytoplasmic 14-3-3.

Several cases have been reported in which proteins are sequestered inthe cytoplasm by binding to 14-3-3, and disruption of this interactionallows the proteins to translocate into the nucleus and perform theirfunction (Brunet et al., 1999; Lopez-Girona et al., 1999; Wang et al.,1999; Yang et al., 1999). It is possible that binding of HDAC4 and HDAC5to 14-3-3 sequesters these proteins in the cytoplasm, where they arepresumably unable to repress transcription. Upon loss of 14-3-3 binding,HDAC4 and HDAC5 could translocate into the nucleus, bind to HDAC3 andMEF2, and repress MEF2-dependent gene expression. In order to study theeffect of 14-3-3 binding on HDAC4 localization, HDAC4-EGFP andmyc-tagged 14-3-3□ were co-expressed in U2OS cells, and the cellularlocalization of HDAC4 was analyzed by immunofluorescence in triplicateexperiments (FIG. 8B). Expression of HDAC4-EGFP alone results in acytoplasmic localization of HDAC4 in 67 (±3) % of the cells, whilesimultaneous overexpression of 14-3-3□ increases this to 97 (±1) % ofthe cells. This correlation suggests that 14-3-3 may play a role insequestering HDAC4 in the cytoplasm.

H. Association of HDAC4 and HDAC5 with 14-3-3 and HDAC3

It is known that 14-3-3 proteins bind to phosphorylated serine orthreonine residues in defined consensus sequences (Rittinger et al.,1999; Yaffe et al., 1997). It was hypothesized that phosphorylation ofHDAC4 and HDAC5 would allow association with 14-3-3 and sequestration inthe cytoplasm. Dephosphorylation of these HDACs should result in theloss of interaction with 14-3-3, with subsequent translocation to thenucleus and binding to HDAC3. To test this hypothesis, the effect ofphosphorylation of HDAC4 and HDAC5 on their association with 14-3-3 andHDAC3 was analyzed.

Recombinant FLAG-tagged HDAC4 and HDAC5 were transiently expressed inTAg Jurkat cells that were subsequently treated with the generalserine/threonine kinase inhibitor staurosporine or the PP1 and PP2Aphosphatase inhibitor calyculin A. The recombinant proteins wereimmunoprecipitated and analyzed by western blot (FIG. 9A). Underdephosphorylating conditions due to staurosporine treatment, there is adecrease in binding of HDAC4 and HDAC5 to either 14-3-3 isoform, and acorresponding increase in HDAC3 association. In addition, an increase inthe overall HDAC activity of the purified complex was observed (FIG.9A). Similarly, under hyper-phosphorylating conditions due to calyculinA treatment, HDAC4 and HDAC5 undergo a notable electrophoretic mobilityshift, probably due to direct phosphorylation. An increase in 14-3-3binding is observed as well, with a concomitant loss of interaction withHDAC3. This loss of binding to HDAC3 presumably causes the dramaticreduction in immunoprecipitated HDAC activity that is observed, thoughthe activity of isolated HDAC4 and HDAC5 is still above background.These data suggest that binding of 14-3-3 to HDAC4 and HDAC5 isdependent on the presence of phosphorylated serine or threonineresidues, and corresponds to a loss of interaction with HDAC3 in thenucleus.

I. Binding of 14-3-3 to HDAC4 Blocks Binding of Importin □

14-3-3 proteins have been shown to sequester Xenopus Cdc25 in thecytoplasm by binding near a bipartite nuclear localization sequence andblocking its interaction with the importin □□ heterodimer (Yang et al.,1999), which is required for import into the nucleus (Gorlich, 1997).HDAC4 also contains a nuclear localization sequence (Hicks and Raikhel,1995). In order to determine if the interaction with 14-3-3 blocksbinding of the importin heterodimer, recombinant FLAG-tagged HDAC4 wasimmunoprecipitated from untreated, staurosporine-, and calyculinA-treated TAg-Jurkat cells and analyzed for binding to importin □ byWestern blotting. Upon binding to 14-3-3 due to calyculin. A treatment,HDAC4 fails to associate with importin □ (FIG. 9B). Thus, sequestrationof HDAC4 and HDAC5 in the cytoplasm by 14-3-3 may be caused by masking anuclear localization sequence.

J. Mutations of the 14-3-3 Binding Sites Cause Increased NuclearLocalization of HDAC4

14-3-3 proteins bind to well-defined consensus sequences containingphosphorylated serine or threonine residues (Rittinger et al., 1999;Yaffe et al., 1997). There are four canonical 14-3-3 binding sites inHDAC4, three of which are well conserved in HDAC5. The serine residuesin each of these three sites in HDAC4 (S246, S466, S632) were mutated toalanine in order to prohibit phosphorylation and thus prevent 14-3-3binding. Mutation of individual sites or two sites is not sufficient toabrogate binding of 14-3-3, but mutation of all three serine residues toalanine (HDAC4 S246/466/632A) abolishes binding to 14-3-3□ and □, evenunder hyperphosphorylating conditions due to calyculin A treatment.Furthermore, localization of the triple mutant to the cytoplasm isdramatically decreased compared to the wild-type and single mutants,consistent with a role for 14-3-3 in sequestration of HDAC4 and HDAC5 inthe cytoplasm.

K. Disruption of HDAC3 and HDAC4 Interaction Upon Calyculin A Treatment

Interestingly, despite its inability to bind 14-3-3 and its concomitantnuclear localization, the HDAC4 S246/466/632A triple mutant is stillunable to bind to HDAC3 under calyculin A treatment. Hence, theinability of HDAC4 to associate with HDAC3 under hyperphosphorylatingconditions cannot simply be due to its sequestration in the cytoplasm.Other possibilities include a change in HDAC4 conformation orelectrostatic properties upon direct phosphorylation that preventsassociation with HDAC3, direct phosphorylation of HDAC3 resulting insimilar alteration in its conformation or electrostatic nature, ormodifications of additional factors that may be required for mediatingthe HDAC4-HDAC3 interaction.

In order to distinguish between these possibilities, immunoprecipitatedHDAC4 from untreated, staurosporine-treated, or calyculin A-treatedcells was incubated with lysates from untreated or calyculin A-treatedTAg Jurkat cells. Briefly, forty-eight hours after transfection withHDAC4-FLAG, TAg Jurkat cells were treated with staurosporine orcalyculin A for 1.5 hours. HDAC4-FLAG was immunopurified and the samplewas split into thirds. One-third of the immunopurified protein wasprepared for Western blot analysis, one-third was incubated for 1 hourwith untreated TAg Jurkat lysate, and the remaining one-third of thesample was incubated with calyculin A-treated TAg Jurkat lysate for 1hour. These samples were analyzed for 14-3-3 and HDAC3 binding byWestern blot analysis. Untreated and staurosporine-treated (presumablyhypophosphorylated) HDAC4 associated with HDAC3 under all conditions,which is consistent with previous observations. Notably, there is anincrease in the amount of associated HDAC3 upon incubation with lysatefrom untreated cells, but not after incubation with lysate from cellstreated with calyculin A. This suggests that HDAC3 from untreated cells,but not from calyculin A-treated cells, is still competent to bindHDAC4. Furthermore, there is no factor in calyculin A-treated cells thatcan disrupt the HDAC4-HDAC3 interaction once it has formed.

As previously observed, calyculin A-treated (hyperphosphorylated) HDAC4does not bind to HDAC3 under normal immunoprecipitation conditions.However, upon incubation with untreated cell lysates, calyculinA-treated HDAC4 does pull down HDAC3. This interaction is not presentupon incubation with calyculin A-treated lysate. Hence, calyculinA-treatment of HDAC4 does not cause it to undergo a conformationalchange that would prevent it from binding to HDAC3. Note that thoughthere does seem to be a slight decrease in the amount of HDAC3 presentin the calyculin A treated lysate, it is not significant enough toexplain the complete lack of binding to HDAC4.

These experiments suggest that while sequestration of HDAC4 in thecytoplasm by 14-3-3 may serve to prevent its interaction with HDAC3,this association is abrogated by an additional mechanism when the cellis exposed to hyperphosphorylating conditions. Since calyculin A-treatedHDAC4 still is capable of association with HDAC3, this loss ofinteraction instead may be due to the phosphorylation of HDAC3 or to themodification of additional proteins required for mediating theHDAC3-HDAC4 association.

L. Increased Nuclear Localization of HDAC4 Enhances MEF2-DependentRepression

The sequestration of HDAC4 and HDAC5 in the cytoplasm by 14-3-3presumably prevents these proteins from repressing gene transcription,and therefore represents a novel mechanism for controlling HDACactivity. In order to determine if cellular localization affectsHDAC4-mediated transcriptional repression by MEF2, the following seriesof reporter gene assays was performed. TAg-Jurkat cells were transfectedwith a MEF2-luciferase reporter, the MEF2D transcription factor, andeither wild-type HDAC4 or the HDAC4 S246/466/632A triple mutant, whichno longer binds to 14-3-3 and displays enhanced nuclear localization.Equivalent expression levels of the wild-type and triple mutant HDAC4recombinant proteins was confirmed by Western blot analysis (data notshown). Expression of wild-type HDAC4 decreases MEF2-dependenttranscription slightly, while expression of the HDAC4 triple mutantcompletely represses transcription. These data are consistent with amodel in which loss of association with 14-3-3 results in nuclearlocalization of HDAC4 and association with MEF2 and HDAC3, causingincreased transcriptional repression.

M. Screening for Specific Inhibitors of Human HDACs

Three classes of histone deacetylase enzymes have been identified inmammalian cells Gray et al. (2001) Exp Cell Res 262:75-83). Class I andClass II HDACs are structurally very similar and possess a conservedcatalytic domain of approximately 390 amino acids (Finnin et al. (1999)Nature 401: 188-93). Of these, four class I (HDAC1, 2, 3 and 8) and fourclass II (HDAC4, 5, 6, 7) have been identified in humans. A third classof seven human histone deacetylases with homology to yeast Sir2 hasrecently been characterized. These HDACs posses a very different primarysequence, and have a conserved catalytic domain of approximately 275 AA.Unlike the class I and class II HDACs, the Sir2 enzymes require NAD as asubstrate for deacetylation. Furthermore, these enzymes are not affectedby any known HDAC inhibitors. Thus, class I and II HDACs presumablyfunction by the same mechanism, while the Sir2 HDACs evolved separatelyand function by a very different mechanism.

The class I and class II HDACs are found in several different proteincomplexes (rev in Ng and Bird (2000) TIBS 25: 121-6; Ahringer (2000)TIGS 16: 351-6) Kao et al (2000) Genes Dev 14: 55-66; Huang et al.(2000) Genes Dev 14: 45-54). With the exception of HDAC6, all of theseHDACs are found in the nucleus (unpublished observations) and presumablyfunction in deacetylating histones and silencing gene expression whenrecruited to chromosomal domains or promoters of specific genes. Severaltranscription factors, including nuclear hormone receptors (Xu et al.(1999) Curr Opin Genet Dev 9: 140-7) and methylated DNA-binding proteins(Ballestar and Wolffe (2001) Eur J Biochem 268: 1-6) have been shown torecruit specific HDAC complexes, but thus far it has not been possibleto determine the complete set of gene targets for each of the HDACs inmammalian cells, since profiling of knockouts have not been reported.Thus, it would be highly advantageous to acquire a set of inhibitorsthat are specific for each of the known class I and class II HDACs.Analysis of the differences in the structures of the HDACs and previousreports of specificity of certain natural and synthetic HDAC inhibitorssuggest that this is a feasible goal.

Structure of Class I and II HDACs

The crystal structure of a bacterial HDAC homolog, HDLP(histone-deacetylase like protein), has been reported (Finnin et al.(1999) Nature 401: 188-93). HDLP has a single domain structure relatedto the open α/β class of folds. It contains a central eight-strandedparallel β-sheet, with four α-helices packed on either face. Eightadditional α-helices and large loops in the β-sheet further extend thestructure, and result in the formation of a deep, narrow pocket, with anadjacent internal cavity. HDLP requires Zn²⁺ for activity, and this zinccation positioned near the bottom of the pocket, which thus presumablyis the active site (see FIG. 10). The active site contains severalaspartate and histidine residues, which appear to function in bothcoordinating the zinc ion and acting as a charge relay system toincrease the nucleophilicity of a bound water molecule, therebyactivating it to attack the amide bond of the acetyl-lysine (see FIG.11). The channel leading to the active site is surrounded by hydrophobicresidues, which is presumably where the aliphatic chain of theacetyl-lysine residue is nestled.

A small molecule inhibitor of histone deacetylases, trichostatin A, hasbeen co-crystallized with HDLP and allows for an analysis of thestructural properties of these inhibitors. TSA contains a cap group, andaliphatic chain and a terminal hydroxamic acid functional group (FIG.12). The hydroxamic acid coordinates the zinc cation in a bidentatefashion and hydrogen bonds with some of the active site residues. Thealiphatic chain fits snugly into the channel, making several van derWaals contacts with the channel residues. The cap group contactsresidues on the rim of the pocket, and probably mimics the amino acidsadjacent to the acetylated lysine residue in the histone. Binding of TSAcauses a conformational change in a tyrosine residue on this rim(Tyr91), thereby allowing tighter packing of the cap group.

The proposed mechanism for the deacetylation reaction is similar to thatseen in metallo- and serine proteases (see FIG. 11). The carbonyl oxygenof the N-acetyl amide bond is thought to coordinate to the zinc cation,thereby positioning it closely to a bound water molecule and activatingit for a nucleophilic attack by the water. The nucleophilicity of thewater molecule, in turn, is enhanced by an interaction with thenegatively charged histidine-arginine pair. Attack of the water moleculeon the carbonyl carbon produces an oxy-anion intermediate, which ispresumably stabilized by interacting with the zinc ion, and possibly byhydrogen bonding to a nearby tyrosine. The collapse of this intermediatewould result in the break of the carbon-nitrogen bond, with the nitrogenaccepting a proton from the histidine residue, and thereby producing theobserved acetate and lysine products.

Structural Differences of the Human HDACs

The catalytic domains of the eight known human HDACs is very wellconserved, but there are certain differences that may allow for theproduction of specific inhibitors. Most of the residues seen in the HDLPstructure that interact directly with TSA are completely conserved amongall of the HDACs, but the conservation in the surrounding residues isless, with significant differences apparent between the class I andclass II HDACs (FIG. 13). Notably, there is significant divergence inthe region of Tyr91 of HDLP, and this tyrosine residue itself is verypoorly conserved among the human HDACs. This is particularly striking inthat this residue is positioned on the rim of the channel and interactsdirectly with the cap group of TSA, and it is the only residue thatshifts its conformation upon TSA binding. Thus, the considerablediversity in the region of the protein interacting with the cap group ofthe inhibitors suggests that it will be possible to develop specificinhibitors by altering the structure of this cap group.

Synthetic HDAC Inhibitors

Several non-natural inhibitors of histone deacetylases have beensynthesized, and analysis of these will facilitate the rational designof novel and specific inhibitors. The basic structure of these smallmolecules mimics that of TSA, in that they possess a cap group, analiphatic chain, and a functional group that would interact with theactive site. It appears that the optimal length for the aliphatic chainis five to six carbon residues, with inhibitory activity decreasingrapidly for longer and shorter chains (Jung et al. (1999) J Med Chem 42:4669-79) There are several possible functional groups, includingepoxides, which appear to form irreversible covalent bonds with activesite residues (see Furumai et al. (2001) Proc Natl Acad Sci USA 98:87-92) as well as hydroxamic acid (Jung et al (1999) J Med Chem 42:4669-79; Furumai (2001) Proc Natl Acad Sci USA 98: 87-92; Richon et al.(1996) Proc Natl Acad Sci USA 93: 57605-8; and Richon et al. (1998) 95:3003-7) and o-aminoanilines (Suzuki et al. (1999) J Med Chem 42: 3001-3)which presumably coordinate the zinc cation. Two types of cap groups arefound in natural HDAC inhibitors, a small flat or linear group or acyclic tetrapeptide. Interestingly, the type of cap group alters theaffinity with which the inhibitor binds to the active site. Moleculeswith a small cap are not active if the functional group is a carboxylicacid, while molecules with cyclic tetrapeptide cap groups and acarboxylic acid functional group are potent inhibitors.

Generation of Specificity

Alterations in the structure of the cap group has led to specificinhibitors of HDACs in two cases. First, N-alkylations of the indoleresidue in the cap group of apicidin has led to the development ofapicidin derivatives that are ˜20-fold more potent inhibitors ofmalarial HDACs than human HDAC1 (Meinke et al. (2000) J Med Chem 43:4919-22). Secondly, HDAC6 is not inhibited by any of the cyclictetrapeptide inhibitors, even when a hydroxamic acid is used as afunctional group. Notably, HDAC6 has the greatest divergence from theother HDACs in the rim region surrounding Tyr91 in HDLP.

Design of Screen

Combinatorial libraries will be screened for specific inhibitors ofHDACs 1, 4 and 6. HDAC1 was chosen to be the representative of the classI HDACs, while HDAC4 is the representative for the class II HDACs. HDAC6will be screened because it is structurally divergent from the otherclass II HDACs, both in primary sequence in the catalytic domain, andthe fact that it has two catalytic domains. Furthermore, HDAC6 isclearly divergent from the other HDACs in that it is not inhibited bythe cyclic tetrapeptide class of inhibitors.

Thus far, an unbiased library (Sternson et al. (2001) J Am Chem Soc 123:1740-7) has been screened for specific inhibitors of these three HDACs.In the future, libraries structurally biased to be similar to known HDACinhibitors will be generated. In these cases, an aliphatic chain with aterminal function group, either a hydroxamic acid, carboxylic acid or ano-aminoaniline, will be attached to a structurally diverse coremolecule. Thus, the diversity will be localized primarily to the capgroup of these potential inhibitors, which is desirable in that changesin this region have been shown to lead to specificity.

Recombinant, purified FLAG-epitope tagged HDAC1 and HDAC6, as well asthe catalytic domain of HDAC4(632-1070) fused to GST were incorporatedin baculovirus vectors and expressed in Sf9 cells. Expression bybaculovirus rather than expression in mammalian cells allowed for theisolation of larger quantities of protein, and also permitted theisolation of these HDACs without associated mammalian proteins. Theseproteins were labeled with Cy5 dye and used to screen a 1200 memberlibrary that had been printed on glass slides (MacBeath et al. (1999) JAm chem Soc 96: 4868-73). The molecules that were identified asreproducibly binding to any of the three HDACs were then tested in asecondary HDAC activity assay (Taunton et al. (1996) Science 272:408-11) None of the identified hits were able to significantly inhibitHDAC activity at 100

Material and Methods

Construction of Baculoviruses

cDNA encoding HDAC1 with a C-terminal FLAG epitope tag was cloned intothe transfer vector pVL1392 (Pharmingen) and used to produce recombinantbaculovirus as described previously (Hassig et al. (1997) Cell 89:341-7). cDNA encoding HDAC6 with a C-terminal FLAG epitope tag wascloned into the NotI/XbaI site of pcDNA6-V5-HisA vector (Invitrogen).This construct, with the C-terminal FLAG, V5, and HisA tags wassubcloned into the NotI/PmeI sites of pVL1392. This construct was usedto generate recombinant baculovirus using the Baculogold DNA, accordingto the manufacturer's instructions (Pharmingen). HDAC4 recombinantbaculovirus was constructed in the pAcSG2T vector, and was obtained fromthe Pavletich group (Memorial Sloan-Kettering Cancer Research Center,New York City). cDNA encoding residues 632 to 1070 of HDAC4 was insertedinto the BamHI and EcoRI sites, in frame with the N-terminal GST codingsequence, separated by a thrombin cut site.

Expression of Protein in Sf9 Cells

Baculovirus was amplified to a concentration of ˜1×10⁶ pfu/ml. Sf9 cellswere infected at a concentration of 1×10⁶ cells/ml, with a multiplicityof infection of 2, at the National Cell Culture Center (Minneapolis,Minn.). 72 hours post-infection, cells infected with HDAC1 and HDAC6baculovirus were pelleted, washed twice in PBS and flash frozen. In thecase of the HDAC4 baculovirus, the protein is secreted into the media,and thus the cells were pelleted and the media saved and stored at 4° C.

Purification of Protein

In the case of GST-HDAC4(632-1070), the protein is secreted into themedia. 500 μl of glutathione-agarose beads were washed in PBS andincubated with 500 mL of media, with shaking for 1.5 hours. The beadswere pelleted (1000 rpm, 5′) and washed twice with cold PBS. The proteinwas eluted with 10 mM glutathione in JLB (50 mM Tris-HCL, pH 8/150 mMNaCl/10% glycerol/0.5% TritonX-100). The beads were incubated twice with1 mL of glutathione/JLB for 20 minutes, and once with 0.5 mL for 10minutes. The collected eluant was dialyzed to remove the glutathione ina 10 kD MWCO Slide-A-Lyzer (Pierce) overnight against 1 L of PBS/10%glycerol/2.5 mM DTT. Note it was necessary to use a buffer without freeamines in order to be compatible with the subsequent Cy5-labelingprocedure.

Pellets of 250 and 100 mL of Sf9 cells infected with HDAC1 and HDAC6baculovirus were lysed in 10 mL of JLB, with incubation at 4 C for 20minutes. The lysate was clarified by pelleting the cellular debris at14,000 rpm for 15 minutes. The protein was immunoprecipitated byincubating with 100 μl of anti-FLAG M2 agarose (Sigma). The beads werewashed three times for three minutes in cold MSWB (50 mM Tris-HCL, pH8/150 mM NaCl/1 mM EDTA/0.1% Nonidet P-40) and the protein was eluted byincubating the beads in 500 μL JLB with 1 mg of FLAG peptide for fourhours. The eluant was collected and the beads washed with 200 μl JLB,which was added to the eluant. The protein was dialyzed overnightagainst JLB in a 10 kD MWCO Slide-A-Lyzer (Pierce). Since this buffercontains amines, it was necessary to exchange the JLB with PBS/10%glycerol/2.5 mM DTT, using a 10 kD MWCO Microcon (Millipore, Bedford,Mass.), according to the manufacturer's instructions.

Expression and Immunoprecipitation of HDACs from Mammalian Cells

Constructs containing HDAC 1 and HDAC6 with C-terminal FLAG epitope tagsin the pBJ5 mammalian expression vector have been described (Grozingeret al. (1999) 96: 4863-73). These were transfected into TAg Jurkat cellsby electroporation, and forty-eight hours later cells were lysed in JLB(50 mM Tris HCl pH 8/150 mM NaCl/10% glycerol/0.5% TritonX-100)containing a complete protease inhibitor cocktail (Boehringer-Mannheim).Lysis proceeded for 10 minutes at 4° C., after which the cellular debriswas pelleted by centrifugation at 14K for 5 minutes. Recombinantproteins were immunoprecipitated from the supernatant by incubation withα-FLAG M2 agarose affinity gel (Sigma) for 1 hours at 4° C. For enzymeactivity assays, the beads were washed three times with JLB at 4° C.

HDAC Assays.

³H-acetate-incorporated histones were isolated from butyrate-treatedHeLa cells by hydroxyapatite chromatography as described (Tong et al.(1998) Nature 395: 917-21). Immunoprecipitates were incubated with 1.4μg (10,000 dpm) histones for three hours at 37° C. HDAC activity wasdetermined by scintillation counting of the ethyl-acetate soluble ³Hacetic acid (Taunton et al. (1996) Science 272: 408-11).

Cy5-Labeling of Proteins

1 mg of Cy5 monofunctional reactive dye (Amersham) was resuspended in 1mL of 50 mM NaCO₃, pH 8.5. Protein was added to this to a concentrationof ˜1 mg/mL, and the reaction was incubated for 1.5 hours at 4° C. Thesolution was dialyzed in a 10 kD MWCO Slide-A-Lyzer (Pierce) against 1 Lof PBS/10% glycerol/2.5 mM DTT overnight, and then against 2 L ofPBS/10% glycerol/2.5 mM DTT/1 mM EDTA for five hours.

Screening of Slides

The 1,3 dioxane library (Sternson et al. (2001) J Am Chem Soc 123:1740-7) was printed on glass slides as described previously. The slideswere blocked for five hours in 3% BSA in PBST (0.1% Tween-20/PBS) andwashed in PBST. Solutions of 400 nM of Cy5-labeled in 1% BSA/PBST werethen added and incubated at 4 C for 1 hour. The slides were washed threetimes with PBST, rinsed with ddH₂O and spun dry (800 rpm, 30 seconds).The slides were scanned on a Applied Precision ArrayWorx scanner.

Results

Expression and Activity of Recombinant HDACs

HDAC1-F, GST-HDAC4(632-1070), and HDAC6-F-V5-HisA were expressed in Sf9cells and purified by FLAG-agarose beads or glutathione agarose. Theseproteins were then labeled with Cy5 dye and purified from the free dyeby dialysis. The purified proteins were subjected to SDS-PAGE andvisualized by silver stain or western blotting with α-FLAG antibody. Allof the proteins expressed well, and there were no contaminants atstoichiometric concentrations apparent from the silver stain, and thusthese are anticipated to be relatively pure. Note that expression in Sf9cells allows for the purification of these proteins in the absence ofthe associated mammalian proteins. This is critical for theidentification of specific HDAC inhibitors, since HDAC1 usuallyassociates with HDAC2 in most mammalian cell lines, while HDAC4associates with HDAC3.

Screening on Printed 1,3 Dioxane Library with Recombinant HDACs

Approximately 2000 compounds from the 1,3 dioxane library were printedon slides (MacBeath et al. (1999) J Am Chem Soc 96: 4868-73) andscreened with the three Cy5-labeled HDACs in triplicate. Compounds thatreproducibly bound these HDACs were identified and their location in thearrayed plates was determined. An example of the observed results for anHDAC6-Cy5 screen (compound 4-P9) is shown in FIG. 15. The followingcompounds were identified in this assay:

HDAC1/HDAC6 common hits: 2-N20, 4-J18, 7-B2, 7-M1, 11-A15

HDAC1 unique hits: 4-H12

HDAC6 unique hits: 2-M7, 4-M9, 4-P9

Retest hits on HDAC1 and HDAC6

FLAG-tagged HDAC1 and HDAC6 were expressed in TAg Jurkat cells andpurified by immunoprecipitation using the anti-FLAG antibody. Note thatTAg Jurkat cells have undetectable quantities of soluble HDAC2, andtherefore HDAC1 that is purified from these cells does not containassociated HDAC2. The proteins were used in in vitro HDAC assays withthe compounds identified in the screen, using concentration ofapproximately 50 μM.

HDAC6 appeared to be inhibited by compound 11-A15, while HDAC1 wasunaffected by it (see FIG. 16). Thus this compound was resynthesized andretested at 100 μM concentration, in triplicate (see results, FIG. 17).It did not inhibit either HDAC at this concentration. Retesting of othercompounds also demonstrated that the previously observed inhibition wasnot reproducible. This suggests that the original results were due tothe low signal-to-noise ratio.

Conclusions

In this screen, three different HDACs were chosen to represent the eightknown human HDAC proteins. Based on sequence similarities, HDAC1 ishighly related to HDACs 2 and 3, while HDAC4 is closely related to HDAC5and 7. HDAC6 is has unique features, both in its sequence and in thefact that it is not inhibited by the cyclic tetrapeptide class of HDACinhibitors.

The methodology outlined above will allow for rapidly screening severalthousand printed compounds for specific binding to any of these threeproteins. Positives identified in this binding assay can easily betested in in vitro HDAC assays with the purified proteins to screen forspecific inhibitory activity. Furthermore, this activity assay can beperformed in very small volumes, and thus resynthesis of the positivecompounds will not be required for this secondary screen.

None of the compounds identified in the binding assay tested positivelyin the subsequent activity assay. This suggests that these compoundswere either false positives or did not bind to the active site of theenzymes. This is not particularly unexpected, since the library that wastested was not structurally biased to mimic HDAC inhibitors. Futurelibraries will include moieties containing an aliphatic side chainterminating with a hydroxamic acid, carboxylic acid, or o-amino anilidegroup. Sample compounds from these libraries have been shown to inhibitHDAC1 activity with an IC₅₀ of 5-100 μM, and thus these will probably bemore suitable for these screens.

Experimental Methods A. Cloning of HDAC4, HDAC5 and HDAC6

The amino acid sequence of yeast Hda1p was used in a tblastn search ofthe NCBI databases to identify human homologs of Hda1p. A cDNA clone forHDAC4 was obtained from the Kazusa DNA Research Institute, Kisarazu,Japan (Gene name KIAA0288, GenBank Accession Number 3024889). The fulllength clone was 8459 bp, with a predicted ORF of 2903 bp. A comparisonof the HDAC4 clone with the HDAC5 sequence, however, revealed that theputative 5′UTR of HDAC4 was highly homologous to the N-terminal codingsequence of HDAC5. A truncation in the HDAC4 ORF seems to have beencaused by a C to T point mutation in the putative 5′UTR of the HDAC4clone, resulting in the conversion of a glutamate codon to a stop codon.This hypothesis was confirmed by obtaining the remaining N-terminal 352bp by PCR from a 5′Stretch cDNA Leukemia Library (Clontech) andsequencing the product. A C-terminal FLAG epitope tag was incorporatedinto the complete HDAC4 ORF of 3255 bp, which was then inserted into theNot I-Eco RI sites of a mammalian expression vector (pBJ5).

An EST (GenBank Accession #R64669) homologous to yHda1p was identifiedand obtained from the I.M.A.G.E. Consortium (Lawrence Livermore NationalLaboratory). This sequence was used to generate a random primed probe(Boehringer Mannheim) to screen a Lambda ZAP II Jurkat cDNA library(Stratagene). A 2.3 kb cDNA clone was identified that contained apartial ORF of HDAC5. A blastn search of the NCBI database facilitatedthe assembly of the full-length cDNA sequence as a combination of asecond clone from the Kazusa DNA Research Institute (Gene Name KIAA0600,GenBank Accession #3043724) and the cDNA clones containing the 11-jsmRNA sequence (GenBank Accession # AF039241), kindly provided by JeffSwensen, (University of Utah). An ORF of 3369 bp was identified andassembled into a C-terminal FLAG construct by subcloning into the NotI-Xho I sites of a pBJ5 vector.

A second EST homologous to yHDA1p was identified and used to screen theLambda ZAP II Jurkat cDNA library. The sequence of the 2.5 kb cloneproduced was used in a blastn search to reveal the full length sequenceof HDAC6 in the jm-21 mRNA sequence (GenBank Accession #AJ011972). Thisinformation was used to obtain the remaining 1.5 kb by nested PCR from a0957 cDNA library, kindly provided by Don Ayer (University of Utah) toproduce the full length ORF of 3648 bp. A C-terminal FLAG epitope tagwas incorporated into this clone, which was inserted into the Not I-SpeI sites of pBJ5.

B. Northern Blot Analysis

Multiple human tissue Northern blots were obtained from Clontech. Probeswere generated and blots were stripped using Strip-EZ DNA probesynthesis and removal kit (Ambion). Prehybridization and hybridizationwas carried out according to manufacturer's instructions usingExpressHyb solution (Clontech). For HDAC4 expression analysis, a 12-lanetissue blot was probed with the 895 bp SalI-SacI fragment of the HDAC4gene. For HDAC5 expression analysis, an 8-lane tissue blot was probedwith the 993 bp SacI-SacII fragment of the HDAC5 gene. This blot wasstripped and reprobed for HDAC6 expression using the 667 bp SphI-AvrIIfragment of the HDAC6 gene. Blots were stripped and reprobed with□-actin cDNA as a control (Clontech).

C. Antibodies, Immunoprecipitation and Western Blotting

Antibodies against HDAC1 (11), HDAC3 (17) and RbAp48 (17) have beendescribed previously. Antibodies against mSin3A were kindly provided byDon Ayer (18), antibodies to the PHD domain of CHD4 were provided byWeidong Wang (National Institute on Aging/NIH) (6) and antibodies to theN-terminal domain of MTA were provided by Yasushi Toh (KyushiUniversity, Fukuoka, Japan) (19, 20).

Forty-eight hours after transfection, cells were lysed in JLB (50 mMTris HCl pH 8/150 mM NaCl/10% glycerol/0.5% TritonX-100) containing acomplete protease inhibitor cocktail (Boehringer-Mannheim). Lysisproceeded for 10 minutes at 4° C., after which the cellular debris waspelleted by centrifugation at 14K for 5 minutes. Recombinant proteinswere immunoprecipitated from the supernatant by incubation with □-FLAGM2 agarose affinity gel (Sigma) for 2 hours at 4° C. For Western blotanalysis, the beads were washed three times for 5 minutes at roomtemperature with MSWB (50 mM Tris HCl pH 8/150 mM NaCl/1 mM EDTA/0.1%NP-40) and the proteins were separated by SDS/PAGE. For enzyme activityassays, the beads were washed three times with JLB at 4° C.

D. HDAC Assays

³H-acetate-incorporated histones were isolated from butyrate-treatedHeLa cells by hydroxyapatite chromatography as described (4).Immunoprecipitates were incubated with 1.4 μg (10,000 dpm) histones forthree hours at 37° C. HDAC activity was determined by scintillationcounting of the ethyl-acetate soluble ³H acetic acid (11). Inhibition ofenzyme activity by trichostatin (TSA) was performed by incubatingsamples with 300 nM TSA (Wako) for 10 minutes prior to addition of thelabeled histones.

E. Histone Isolation and Substrate Specificity Determination

For deacetylase assays, 6 □g of histones were incubated withimmunoprecipitated recombinant enzyme or negative control (RbAp48transfected) for 3 hours at 37° C. in HD buffer (50 mM Tris, pH 8.0/150mM NaCl/10% glycerol). Reactions were stopped with SDS loading bufferand proteins were separated by 20% SDS/PAGE.

F. HDAC6 Mutagenesis

The H216A and H611A mutations were produced by PCR overlap extension.For each mutant, internal primers to both strands with the correspondingCAC to GCC mismatches were synthesized and used to amplify twooverlapping fragments containing the mutation in the common region.These fragments were then used as templates in a second PCR reactionwith the same flanking external primers. The H216A fragment was ligatedinto the Not I and Dra III sites of the wild-type HDAC6-pBJ5 construct.The H611A fragment was ligated into the Dra III and BstE II sites of thewild-type HDAC6-pBJ5. The H216/611A double mutant was constructed byligating the H216A fragment into the Not I and Dra III sites of theHDAC6-H611A-pBJ5 clone. Plasmids were sequenced to ensure theincorporation of the mutations.

G. Cell Culture and Transfections

TAg-Jurkat cells were transfected by electroporation with 5 μg ofFLAG-epitope tagged pBJ5 constructs for expression of recombinantproteins. Cells were mock-transfected without DNA or with an untaggedRbAp48 construct in pBJ5 as a negative control. Cells were harvested 48hours post-transfection.

H. DNA Constructs

FLAG-epitope-tagged HDAC4 and HDAC5 constructs in the pBJ5 mammalianexpression vector have been described previously (Grozinger et al,1999). The HDAC4-EGFP clone in pBJ5 was made by ligation of a Not I-XbaI HDAC4-FLAG fragment to a Xba I-Sal I EGFP fragment, which wasgenerated by PCR from a plasmid containing EGFP (Clontech). TheHDAC5-EGFP/pBJ5 construct was made similarly using Not I-Xba IHDAC5-FLAG fragment. The C-terminally-myc-epitope-tagged 14-3-3□ wasproduced by PCR from a Jurkat cDNA library (Stratagene) and subclonedinto the Not I and Spe I sites of pBJ5.

The S246A, S466A and S632A single, double and triple mutations in HDAC4were generated by PCR overlap extension. For each mutant, internalprimers to each complementary strand with the corresponding base pairmismatches were synthesized and used to amplify two overlappingfragments containing the mutations in the common region. These fragmentswere then used in a second PCR with the same flanking external primers.The sequence of the primers used will be made available on request. Thefragments were cloned into the Not I and Sac II sites of theHDAC4-F/pBJ5 construct and sequenced to ensure proper incorporation ofthe mutations.

The reporter used in the luciferase assays contains three copies of thedesmin MEF2 site in pGL2-E1b-Luciferase and was generously provided byEric Olson (University of Texas, Southwestern Medical Center). Themyc-epitope-tagged. MEF2D/pSCT mammalian expression plasmid was kindlyprovided by Jun Liu (MIT).

I. Antibodies, Immunoprecipitation and Western Blotting

Antibodies against HDAC3 have been described previously (Hassig et al.,1998). Isoform-specific antibodies against 14-3-3□ and □ were obtainedfrom Santa Cruz Biotechnology, while antibodies to importin □0 (□-Rch1)were acquired from Transducin Laboratories. □-FLAG M2 antibodies and□-mouse IgG Texas-red conjugated secondary antibodies forimmunofluorescence were obtained from Sigma, while □-c-myc antibodieswere purchased from Upstate Biotechnology.

Forty-eight hours after transfection, cells were lysed in JLB (50 mMTris HCl pH 8/150 mM NaCl/10% glycerol/0.5% TritonX-100) containing acomplete protease inhibitor cocktail (Boehringer-Mannheim) andphosphatase inhibitors (20 mM NaH₂(PO₄), pH 7.2; 25 mM NaF, 2 mM EDTA).Lysis proceeded for 10 minutes at 4° C., after which the cellular debriswas pelleted by centrifugation at 14K for 5 minutes. Recombinantproteins were immunoprecipitated from the supernatant by incubation with□-FLAG M2 agarose affinity gel (Sigma) for 1 hour at 4° C. For Westernblot analysis and silver staining, the beads were washed three times for5 minutes at room temperature with MSWB (50 mM Tris HCl pH 8/150 mMNaCl/1 mM EDTA/0.1% NP-40) and the proteins were separated by SDS/PAGE.For enzyme activity assays, the beads were washed three times with JLBat 4° C.

J. Peptide Microsequencing

The sequence analysis was performed at the Harvard MicrochemistryFacility by microcapillary reverse-phase HPLC nano-electrospray tandemmass spectrometry (□LC/MS/MS) on a Finnigan LCQ quadropole ion trap massspectrometer,

K. HDAC Assays

[³H]-acetate-incorporated histones were isolated from butyrate-treatedHeLa cells by hydroxyapatite chromatography as described (Tong et al.,1998). Immunoprecipitates were incubated with 1.4 μg (10,000 dpm)histones for two hours at 37° C. HDAC activity was determined byscintillation counting of the ethyl-acetate soluble [³H]acetic acid(Taunton et al., 1996).

L. Cell Culture and Transfections

TAg-Jurkat cells were transfected by electroporation with 5 μg of DNAfor expression of recombinant proteins, or mock-transfected without DNAas a negative control. Cells were harvested 48 hours post-transfection.When required, cells were treated with 200 □M staurosporin (Calbiochem)or 20 nM calyculin A (Calbiochem) for 1.5 hours prior to harvesting.

M. Immunofluorescence

Cos-7 or U20S cells were plated on coverslips and allowed to attachovernight. Subsequently they were transfected with 1-2 □g of DNA usingthe Lipofectamine PLUS system (Gibco). Forty-eight hours later, cellswere fixed with paraformaldehyde and stained with antibodies and Hoechstdye (Molecular Probes), or live cells were stained with Hoechst and theEGFP was visualized directly using an fluorescence microscope (SpencerScientific Corporation). For the time course studies, a Delta Visionconfocal microscope (Applied Precision Technologies) was used.

N. Reporter Gene Assays

For each sample, 10 million TAg Jurkat cells were transfected with atotal of 5 □g of DNA. A constitutive □-galactosidase expression vectorwas used as a control for protein expression levels in the luciferaseassays. Thirty-eight hours after transfection, the samples wereharvested and split into sets of three. Luciferase activity wasdetermined according manufacturer's instructions (Promega), and□-galactosidase activity was determined using a standard □-galactosidaseassay. Luciferase values (relative light units) were normalized fortransfection efficiency by dividing by □-gal activity. These assays wereperformed four times with similar results.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, numerous equivalents to thespecific polypeptides, nucleic acids, methods, assays and reagentsdescribed herein. Such equivalents are considered to be within the scopeof this invention and are covered by the following claims.

We claim:
 1. A polypeptide comprising an amino acid sequence identicalto SEQ ID NO: 4 fused to a heterologous polypeptide and/or fused to anepitope tag.
 2. The polypeptide of claim 1, wherein the polypeptide hasdeacetylase activity.
 3. The polypeptide of claim 1, wherein thepolypeptide binds to a histone, a 14-3-3 protein, a MEF2 transcriptionfactor, or a retinoblastoma associated protein.
 4. The polypeptide ofclaim 3, wherein the retinoblastoma associated protein is RbAp48.
 5. Thepolypeptide of claim 1, wherein the heterologous polypeptide comprisesglutathione-S-transferase.
 6. The polypeptide of claim 1, wherein theheterologous polypeptide comprises a fluorescent protein.
 7. Thepolypeptide of claim 1, wherein the heterologous polypeptide comprises agreen fluorescent protein.
 8. The polypeptide of claim 1, wherein thepolypeptide has a molecular weight ranging from 80 kDa to 150 kDa. 9.The polypeptide of claim 1, wherein the polypeptide retains one or moreof a histone deacetylase activity or a histone binding activity.
 10. Thepolypeptide of claim 1, wherein the polypeptide modulates cellularproliferation.
 11. The polypeptide of claim 1, wherein the polypeptidecomprises an amino acid sequence identical to SEQ ID NO: 4 fused to anepitope tag.
 12. The polypeptide of claim 11, wherein the epitope tag isa FLAG, V5, or HisA tag.
 13. The polypeptide of claim 1, wherein theheterologous polypeptide comprises an immunoglobulin.
 14. Thepolypeptide of claim 13, wherein the epitope tag is a HisA tag.
 15. Thepolypeptide of claim 5, wherein the polypeptide is adsorbed ontoglutathione sepharose beads or glutathione derivatized microtitreplates.
 16. The polypeptide of claim 1, wherein the heterologouspolypeptide is streptavidin.
 17. A polypeptide comprising an amino acidsequence identical to SEQ ID NO: 4 fused to a biotin moiety.
 18. Apolypeptide consisting of an amino acid sequence identical to SEQ ID NO:9 fused to glutathione-S-transferase.
 19. A composition comprising thepolypeptide of claim 1 and a carrier.
 20. An assay for screening testcompounds to identify agents which inhibit the deacetylation of histonescomprising: providing a reaction mixture comprising the polypeptide ofclaim 1 and a test compound, wherein conversion of substrate to productin the reaction mixture is indicative of histone deacetylase activity;and determining the extent of conversion of substrate to product in thereaction mixture in the presence of a test compound, wherein astatistically significant decrease in the conversion of the substrate inthe presence of the test compound indicates that the test compound is apotential inhibitor of histone deacetylation.
 21. An assay for screeningtest compounds to identify agents which inhibit the deacetylation ofhistones comprising: providing a reaction mixture comprising thepolypeptide of claim 11 and a spatially segregated combinatorial smallmolecule library; and detecting the presence of the polypeptide of claim11 bound at a specific position of the spatially segregatedcombinatorial small molecule library, wherein the position indicates theidentity of the small molecule inhibitor, thereby identifying an agentwhich inhibits the deacetylation of histones.
 22. An assay for screeningtest compounds to identify agents which inhibit histone deacetylaseinteraction with cellular proteins comprising: providing a reactionmixture comprising the polypeptide of claim 1, a histone deacetylasebinding protein, and a test compound; and detecting the interaction ofthe polypeptide of claim 1 and the histone deacetylase binding protein,wherein a statistically significant decrease in the interaction of thepolypeptide of claim 1 and the histone deacetylase binding protein inthe presence of the test compound indicates that the test compound is apotential inhibitor of histone deacetylation.
 23. The assay of claim 22,wherein the histone deacetylase binding protein is selected from: ahistone, a 14-3-3 protein, a MEF2 transcription factor, and aretinoblastoma associated protein.